From 92ef528f54e8a7e8645e1986d4898ad677ba9521 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Tue, 1 Nov 2022 09:39:53 -0400
Subject: [PATCH 001/114] working on ashlar nextflow module outside nf-core
 template.  Input and output working.

---
 modules/nf-core/ashlar/ashlar.nf |   88 +
 tests/config/pytest_modules.yml  | 2920 +++++++++++++++---------------
 2 files changed, 1550 insertions(+), 1458 deletions(-)
 create mode 100644 modules/nf-core/ashlar/ashlar.nf

diff --git a/modules/nf-core/ashlar/ashlar.nf b/modules/nf-core/ashlar/ashlar.nf
new file mode 100644
index 00000000000..540708919e9
--- /dev/null
+++ b/modules/nf-core/ashlar/ashlar.nf
@@ -0,0 +1,88 @@
+params.str = 'Hello world!'
+
+process splitLetters {
+  output:
+    path 'chunk_*'
+
+  """
+  printf '${params.str}' | split -b 6 - chunk_
+  """
+}
+
+process convertToUpper {
+  input:
+    path x
+  output:
+    stdout
+
+  """
+  cat $x | tr '[a-z]' '[A-Z]'
+  """
+}
+
+process ashlar_works_1 {
+    conda 'bioconda::ashlar=1.17.0'
+
+    input:
+        path file_in
+    output:
+        stdout
+
+    """
+    ashlar $file_in -o foo.ome.tif
+    """
+
+    /*
+    output:
+        stdout
+    """
+    ashlar --help
+    """
+    */
+}
+
+process ashlar_works_2 {
+    conda 'bioconda::ashlar=1.17.0'
+
+    input:
+        path file_in
+    output:
+        stdout
+
+    """
+    ashlar $file_in -o $params.out
+    """
+
+}
+
+process wc {
+    input:
+        path file_in
+    output:
+        stdout
+
+    """
+        wc -l $file_in
+    """
+}
+
+process ashlar {
+    conda 'bioconda::ashlar=1.17.0'
+
+    input:
+        path file_in
+    output:
+        path '*.ome.tif'
+
+    """
+    ashlar $file_in -o $params.out
+    """
+
+}
+
+workflow {
+  // splitLetters | flatten | convertToUpper | view { it.trim() }
+  // ashlar(params.in) | view { it.trim() }
+  //wc(params.in) | view { it.trim() }
+  ashlar(params.in) | wc | view { it.trim() }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 80c3ce85ae2..ef3f7c81b5b 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1,2881 +1,2885 @@
 abacas:
-  - modules/nf-core/abacas/**
-  - tests/modules/nf-core/abacas/**
+- modules/nf-core/abacas/**
+- tests/modules/nf-core/abacas/**
 
 abricate/run:
-  - modules/nf-core/abricate/run/**
-  - tests/modules/nf-core/abricate/run/**
+- modules/nf-core/abricate/run/**
+- tests/modules/nf-core/abricate/run/**
 
 abricate/summary:
-  - modules/nf-core/abricate/summary/**
-  - tests/modules/nf-core/abricate/summary/**
+- modules/nf-core/abricate/summary/**
+- tests/modules/nf-core/abricate/summary/**
 
 adapterremoval:
-  - modules/nf-core/adapterremoval/**
-  - tests/modules/nf-core/adapterremoval/**
+- modules/nf-core/adapterremoval/**
+- tests/modules/nf-core/adapterremoval/**
 
 adapterremovalfixprefix:
-  - modules/nf-core/adapterremovalfixprefix/**
-  - tests/modules/nf-core/adapterremovalfixprefix/**
+- modules/nf-core/adapterremovalfixprefix/**
+- tests/modules/nf-core/adapterremovalfixprefix/**
 
 agrvate:
-  - modules/nf-core/agrvate/**
-  - tests/modules/nf-core/agrvate/**
+- modules/nf-core/agrvate/**
+- tests/modules/nf-core/agrvate/**
 
 allelecounter:
-  - modules/nf-core/allelecounter/**
-  - tests/modules/nf-core/allelecounter/**
+- modules/nf-core/allelecounter/**
+- tests/modules/nf-core/allelecounter/**
 
 ampir:
-  - modules/nf-core/ampir/**
-  - tests/modules/nf-core/ampir/**
+- modules/nf-core/ampir/**
+- tests/modules/nf-core/ampir/**
 
 amplify/predict:
-  - modules/nf-core/amplify/predict/**
-  - tests/modules/nf-core/amplify/predict/**
+- modules/nf-core/amplify/predict/**
+- tests/modules/nf-core/amplify/predict/**
 
 amps:
-  - modules/nf-core/amps/**
-  - tests/modules/nf-core/amps/**
+- modules/nf-core/amps/**
+- tests/modules/nf-core/amps/**
 
 amrfinderplus/run:
-  - modules/nf-core/amrfinderplus/run/**
-  - tests/modules/nf-core/amrfinderplus/run/**
+- modules/nf-core/amrfinderplus/run/**
+- tests/modules/nf-core/amrfinderplus/run/**
 
 amrfinderplus/update:
-  - modules/nf-core/amrfinderplus/update/**
-  - tests/modules/nf-core/amrfinderplus/update/**
+- modules/nf-core/amrfinderplus/update/**
+- tests/modules/nf-core/amrfinderplus/update/**
 
 angsd/docounts:
-  - modules/nf-core/angsd/docounts/**
-  - tests/modules/nf-core/angsd/docounts/**
+- modules/nf-core/angsd/docounts/**
+- tests/modules/nf-core/angsd/docounts/**
 
 antismash/antismashlite:
-  - modules/nf-core/antismash/antismashlite/**
-  - tests/modules/nf-core/antismash/antismashlite/**
+- modules/nf-core/antismash/antismashlite/**
+- tests/modules/nf-core/antismash/antismashlite/**
 
 antismash/antismashlitedownloaddatabases:
-  - modules/nf-core/antismash/antismashlitedownloaddatabases/**
-  - tests/modules/nf-core/antismash/antismashlitedownloaddatabases/**
+- modules/nf-core/antismash/antismashlitedownloaddatabases/**
+- tests/modules/nf-core/antismash/antismashlitedownloaddatabases/**
 
 aria2:
-  - modules/nf-core/aria2/**
-  - tests/modules/nf-core/aria2/**
+- modules/nf-core/aria2/**
+- tests/modules/nf-core/aria2/**
 
 ariba/getref:
-  - modules/nf-core/ariba/getref/**
-  - tests/modules/nf-core/ariba/getref/**
+- modules/nf-core/ariba/getref/**
+- tests/modules/nf-core/ariba/getref/**
 
 ariba/run:
-  - modules/nf-core/ariba/run/**
-  - tests/modules/nf-core/ariba/run/**
+- modules/nf-core/ariba/run/**
+- tests/modules/nf-core/ariba/run/**
 
 arriba:
-  - modules/nf-core/arriba/**
-  - tests/modules/nf-core/arriba/**
+- modules/nf-core/arriba/**
+- tests/modules/nf-core/arriba/**
 
 artic/guppyplex:
-  - modules/nf-core/artic/guppyplex/**
-  - tests/modules/nf-core/artic/guppyplex/**
+- modules/nf-core/artic/guppyplex/**
+- tests/modules/nf-core/artic/guppyplex/**
 
 artic/minion:
-  - modules/nf-core/artic/minion/**
-  - tests/modules/nf-core/artic/minion/**
+- modules/nf-core/artic/minion/**
+- tests/modules/nf-core/artic/minion/**
 
 ascat:
-  - modules/nf-core/ascat/**
-  - tests/modules/nf-core/ascat/**
+- modules/nf-core/ascat/**
+- tests/modules/nf-core/ascat/**
+
+ashlar:
+- modules/nf-core/ashlar/**
+- tests/modules/nf-core/ashlar/**
 
 assemblyscan:
-  - modules/nf-core/assemblyscan/**
-  - tests/modules/nf-core/assemblyscan/**
+- modules/nf-core/assemblyscan/**
+- tests/modules/nf-core/assemblyscan/**
 
 ataqv/ataqv:
-  - modules/nf-core/ataqv/ataqv/**
-  - tests/modules/nf-core/ataqv/ataqv/**
+- modules/nf-core/ataqv/ataqv/**
+- tests/modules/nf-core/ataqv/ataqv/**
 
 ataqv/mkarv:
-  - modules/nf-core/ataqv/mkarv/**
-  - tests/modules/nf-core/ataqv/mkarv/**
+- modules/nf-core/ataqv/mkarv/**
+- tests/modules/nf-core/ataqv/mkarv/**
 
 atlas/call:
-  - modules/nf-core/atlas/call/**
-  - tests/modules/nf-core/atlas/call/**
+- modules/nf-core/atlas/call/**
+- tests/modules/nf-core/atlas/call/**
 
 atlas/pmd:
-  - modules/nf-core/atlas/pmd/**
-  - tests/modules/nf-core/atlas/pmd/**
+- modules/nf-core/atlas/pmd/**
+- tests/modules/nf-core/atlas/pmd/**
 
 atlas/recal:
-  - modules/nf-core/atlas/recal/**
-  - tests/modules/nf-core/atlas/recal/**
+- modules/nf-core/atlas/recal/**
+- tests/modules/nf-core/atlas/recal/**
 
 atlas/splitmerge:
-  - modules/nf-core/atlas/splitmerge/**
-  - tests/modules/nf-core/atlas/splitmerge/**
+- modules/nf-core/atlas/splitmerge/**
+- tests/modules/nf-core/atlas/splitmerge/**
 
 atlasgeneannotationmanipulation/gtf2featureannotation:
-  - modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/**
-  - tests/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/**
+- modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/**
+- tests/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/**
 
 bakta:
-  - modules/nf-core/bakta/**
-  - tests/modules/nf-core/bakta/**
+- modules/nf-core/bakta/**
+- tests/modules/nf-core/bakta/**
 
 bamaligncleaner:
-  - modules/nf-core/bamaligncleaner/**
-  - tests/modules/nf-core/bamaligncleaner/**
+- modules/nf-core/bamaligncleaner/**
+- tests/modules/nf-core/bamaligncleaner/**
 
 bamcmp:
-  - modules/nf-core/bamcmp/**
-  - tests/modules/nf-core/bamcmp/**
+- modules/nf-core/bamcmp/**
+- tests/modules/nf-core/bamcmp/**
 
 bamtools/convert:
-  - modules/nf-core/bamtools/convert/**
-  - tests/modules/nf-core/bamtools/convert/**
+- modules/nf-core/bamtools/convert/**
+- tests/modules/nf-core/bamtools/convert/**
 
 bamtools/split:
-  - modules/nf-core/bamtools/split/**
-  - tests/modules/nf-core/bamtools/split/**
+- modules/nf-core/bamtools/split/**
+- tests/modules/nf-core/bamtools/split/**
 
 bamtools/stats:
-  - modules/nf-core/bamtools/stats/**
-  - tests/modules/nf-core/bamtools/stats/**
+- modules/nf-core/bamtools/stats/**
+- tests/modules/nf-core/bamtools/stats/**
 
 bamutil/trimbam:
-  - modules/nf-core/bamutil/trimbam/**
-  - tests/modules/nf-core/bamutil/trimbam/**
+- modules/nf-core/bamutil/trimbam/**
+- tests/modules/nf-core/bamutil/trimbam/**
 
 bandage/image:
-  - modules/nf-core/bandage/image/**
-  - tests/modules/nf-core/bandage/image/**
+- modules/nf-core/bandage/image/**
+- tests/modules/nf-core/bandage/image/**
 
 bases2fastq:
-  - modules/nf-core/bases2fastq/**
-  - tests/modules/nf-core/bases2fastq/**
+- modules/nf-core/bases2fastq/**
+- tests/modules/nf-core/bases2fastq/**
 
 bbmap/align:
-  - modules/nf-core/bbmap/align/**
-  - tests/modules/nf-core/bbmap/align/**
+- modules/nf-core/bbmap/align/**
+- tests/modules/nf-core/bbmap/align/**
 
 bbmap/bbduk:
-  - modules/nf-core/bbmap/bbduk/**
-  - tests/modules/nf-core/bbmap/bbduk/**
+- modules/nf-core/bbmap/bbduk/**
+- tests/modules/nf-core/bbmap/bbduk/**
 
 bbmap/bbsplit:
-  - modules/nf-core/bbmap/bbsplit/**
-  - tests/modules/nf-core/bbmap/bbsplit/**
+- modules/nf-core/bbmap/bbsplit/**
+- tests/modules/nf-core/bbmap/bbsplit/**
 
 bbmap/clumpify:
-  - modules/nf-core/bbmap/clumpify/**
-  - tests/modules/nf-core/bbmap/clumpify/**
+- modules/nf-core/bbmap/clumpify/**
+- tests/modules/nf-core/bbmap/clumpify/**
 
 bbmap/index:
-  - modules/nf-core/bbmap/index/**
-  - tests/modules/nf-core/bbmap/index/**
+- modules/nf-core/bbmap/index/**
+- tests/modules/nf-core/bbmap/index/**
 
 bbmap/pileup:
-  - modules/nf-core/bbmap/pileup/**
-  - tests/modules/nf-core/bbmap/pileup/**
+- modules/nf-core/bbmap/pileup/**
+- tests/modules/nf-core/bbmap/pileup/**
 
 bcftools/annotate:
-  - modules/nf-core/bcftools/annotate/**
-  - tests/modules/nf-core/bcftools/annotate/**
+- modules/nf-core/bcftools/annotate/**
+- tests/modules/nf-core/bcftools/annotate/**
 
 bcftools/concat:
-  - modules/nf-core/bcftools/concat/**
-  - tests/modules/nf-core/bcftools/concat/**
+- modules/nf-core/bcftools/concat/**
+- tests/modules/nf-core/bcftools/concat/**
 
 bcftools/consensus:
-  - modules/nf-core/bcftools/consensus/**
-  - tests/modules/nf-core/bcftools/consensus/**
+- modules/nf-core/bcftools/consensus/**
+- tests/modules/nf-core/bcftools/consensus/**
 
 bcftools/convert:
-  - modules/nf-core/bcftools/convert/**
-  - tests/modules/nf-core/bcftools/convert/**
+- modules/nf-core/bcftools/convert/**
+- tests/modules/nf-core/bcftools/convert/**
 
 bcftools/filter:
-  - modules/nf-core/bcftools/filter/**
-  - tests/modules/nf-core/bcftools/filter/**
+- modules/nf-core/bcftools/filter/**
+- tests/modules/nf-core/bcftools/filter/**
 
 bcftools/index:
-  - modules/nf-core/bcftools/index/**
-  - tests/modules/nf-core/bcftools/index**
+- modules/nf-core/bcftools/index/**
+- tests/modules/nf-core/bcftools/index**
 
 bcftools/isec:
-  - modules/nf-core/bcftools/isec/**
-  - tests/modules/nf-core/bcftools/isec/**
+- modules/nf-core/bcftools/isec/**
+- tests/modules/nf-core/bcftools/isec/**
 
 bcftools/merge:
-  - modules/nf-core/bcftools/merge/**
-  - tests/modules/nf-core/bcftools/merge/**
+- modules/nf-core/bcftools/merge/**
+- tests/modules/nf-core/bcftools/merge/**
 
 bcftools/mpileup:
-  - modules/nf-core/bcftools/mpileup/**
-  - tests/modules/nf-core/bcftools/mpileup/**
+- modules/nf-core/bcftools/mpileup/**
+- tests/modules/nf-core/bcftools/mpileup/**
 
 bcftools/norm:
-  - modules/nf-core/bcftools/norm/**
-  - tests/modules/nf-core/bcftools/norm/**
+- modules/nf-core/bcftools/norm/**
+- tests/modules/nf-core/bcftools/norm/**
 
 bcftools/query:
-  - modules/nf-core/bcftools/query/**
-  - tests/modules/nf-core/bcftools/query/**
+- modules/nf-core/bcftools/query/**
+- tests/modules/nf-core/bcftools/query/**
 
 bcftools/reheader:
-  - modules/nf-core/bcftools/reheader/**
-  - tests/modules/nf-core/bcftools/reheader/**
+- modules/nf-core/bcftools/reheader/**
+- tests/modules/nf-core/bcftools/reheader/**
 
 bcftools/roh:
-  - modules/nf-core/bcftools/roh/**
-  - tests/modules/nf-core/bcftools/roh/**
+- modules/nf-core/bcftools/roh/**
+- tests/modules/nf-core/bcftools/roh/**
 
 bcftools/sort:
-  - modules/nf-core/bcftools/sort/**
-  - tests/modules/nf-core/bcftools/sort/**
+- modules/nf-core/bcftools/sort/**
+- tests/modules/nf-core/bcftools/sort/**
 
 bcftools/stats:
-  - modules/nf-core/bcftools/stats/**
-  - tests/modules/nf-core/bcftools/stats/**
+- modules/nf-core/bcftools/stats/**
+- tests/modules/nf-core/bcftools/stats/**
 
 bcftools/view:
-  - modules/nf-core/bcftools/view/**
-  - tests/modules/nf-core/bcftools/view/**
+- modules/nf-core/bcftools/view/**
+- tests/modules/nf-core/bcftools/view/**
 
 bcl2fastq:
-  - modules/nf-core/bcl2fastq/**
-  - tests/modules/nf-core/bcl2fastq/**
+- modules/nf-core/bcl2fastq/**
+- tests/modules/nf-core/bcl2fastq/**
 
 bclconvert:
-  - modules/nf-core/bclconvert/**
-  - tests/modules/nf-core/bclconvert/**
+- modules/nf-core/bclconvert/**
+- tests/modules/nf-core/bclconvert/**
 
 bedtools/bamtobed:
-  - modules/nf-core/bedtools/bamtobed/**
-  - tests/modules/nf-core/bedtools/bamtobed/**
+- modules/nf-core/bedtools/bamtobed/**
+- tests/modules/nf-core/bedtools/bamtobed/**
 
 bedtools/closest:
-  - modules/nf-core/bedtools/closest/**
-  - tests/modules/nf-core/bedtools/closest/**
+- modules/nf-core/bedtools/closest/**
+- tests/modules/nf-core/bedtools/closest/**
 
 bedtools/complement:
-  - modules/nf-core/bedtools/complement/**
-  - tests/modules/nf-core/bedtools/complement/**
+- modules/nf-core/bedtools/complement/**
+- tests/modules/nf-core/bedtools/complement/**
 
 bedtools/coverage:
-  - modules/nf-core/bedtools/coverage/**
-  - tests/modules/nf-core/bedtools/coverage/**
+- modules/nf-core/bedtools/coverage/**
+- tests/modules/nf-core/bedtools/coverage/**
 
 bedtools/genomecov:
-  - modules/nf-core/bedtools/genomecov/**
-  - tests/modules/nf-core/bedtools/genomecov/**
+- modules/nf-core/bedtools/genomecov/**
+- tests/modules/nf-core/bedtools/genomecov/**
 
 bedtools/getfasta:
-  - modules/nf-core/bedtools/getfasta/**
-  - tests/modules/nf-core/bedtools/getfasta/**
+- modules/nf-core/bedtools/getfasta/**
+- tests/modules/nf-core/bedtools/getfasta/**
 
 bedtools/intersect:
-  - modules/nf-core/bedtools/intersect/**
-  - tests/modules/nf-core/bedtools/intersect/**
+- modules/nf-core/bedtools/intersect/**
+- tests/modules/nf-core/bedtools/intersect/**
 
 bedtools/makewindows:
-  - modules/nf-core/bedtools/makewindows/**
-  - tests/modules/nf-core/bedtools/makewindows/**
+- modules/nf-core/bedtools/makewindows/**
+- tests/modules/nf-core/bedtools/makewindows/**
 
 bedtools/maskfasta:
-  - modules/nf-core/bedtools/maskfasta/**
-  - tests/modules/nf-core/bedtools/maskfasta/**
+- modules/nf-core/bedtools/maskfasta/**
+- tests/modules/nf-core/bedtools/maskfasta/**
 
 bedtools/merge:
-  - modules/nf-core/bedtools/merge/**
-  - tests/modules/nf-core/bedtools/merge/**
+- modules/nf-core/bedtools/merge/**
+- tests/modules/nf-core/bedtools/merge/**
 
 bedtools/slop:
-  - modules/nf-core/bedtools/slop/**
-  - tests/modules/nf-core/bedtools/slop/**
+- modules/nf-core/bedtools/slop/**
+- tests/modules/nf-core/bedtools/slop/**
 
 bedtools/sort:
-  - modules/nf-core/bedtools/sort/**
-  - tests/modules/nf-core/bedtools/sort/**
+- modules/nf-core/bedtools/sort/**
+- tests/modules/nf-core/bedtools/sort/**
 
 bedtools/split:
-  - modules/nf-core/bedtools/split/**
-  - tests/modules/nf-core/bedtools/split/**
+- modules/nf-core/bedtools/split/**
+- tests/modules/nf-core/bedtools/split/**
 
 bedtools/subtract:
-  - modules/nf-core/bedtools/subtract/**
-  - tests/modules/nf-core/bedtools/subtract/**
+- modules/nf-core/bedtools/subtract/**
+- tests/modules/nf-core/bedtools/subtract/**
 
 biobambam/bammarkduplicates2:
-  - modules/nf-core/biobambam/bammarkduplicates2/**
-  - tests/modules/nf-core/biobambam/bammarkduplicates2/**
+- modules/nf-core/biobambam/bammarkduplicates2/**
+- tests/modules/nf-core/biobambam/bammarkduplicates2/**
 
 biobambam/bammerge:
-  - modules/nf-core/biobambam/bammerge/**
-  - tests/modules/nf-core/biobambam/bammerge/**
+- modules/nf-core/biobambam/bammerge/**
+- tests/modules/nf-core/biobambam/bammerge/**
 
 biobambam/bamsormadup:
-  - modules/nf-core/biobambam/bamsormadup/**
-  - tests/modules/nf-core/biobambam/bamsormadup/**
+- modules/nf-core/biobambam/bamsormadup/**
+- tests/modules/nf-core/biobambam/bamsormadup/**
 
 biohansel:
-  - modules/nf-core/biohansel/**
-  - tests/modules/nf-core/biohansel/**
+- modules/nf-core/biohansel/**
+- tests/modules/nf-core/biohansel/**
 
 biscuit/align:
-  - modules/nf-core/biscuit/index/**
-  - modules/nf-core/biscuit/align/**
-  - tests/modules/nf-core/biscuit/align/**
+- modules/nf-core/biscuit/index/**
+- modules/nf-core/biscuit/align/**
+- tests/modules/nf-core/biscuit/align/**
 
 biscuit/biscuitblaster:
-  - modules/nf-core/biscuit/index/**
-  - modules/nf-core/biscuit/biscuitblaster/**
-  - tests/modules/nf-core/biscuit/biscuitblaster/**
+- modules/nf-core/biscuit/index/**
+- modules/nf-core/biscuit/biscuitblaster/**
+- tests/modules/nf-core/biscuit/biscuitblaster/**
 
 biscuit/bsconv:
-  - modules/nf-core/biscuit/index/**
-  - modules/nf-core/biscuit/bsconv/**
-  - tests/modules/nf-core/biscuit/bsconv/**
+- modules/nf-core/biscuit/index/**
+- modules/nf-core/biscuit/bsconv/**
+- tests/modules/nf-core/biscuit/bsconv/**
 
 biscuit/epiread:
-  - modules/nf-core/biscuit/index/**
-  - modules/nf-core/biscuit/epiread/**
-  - tests/modules/nf-core/biscuit/epiread/**
+- modules/nf-core/biscuit/index/**
+- modules/nf-core/biscuit/epiread/**
+- tests/modules/nf-core/biscuit/epiread/**
 
 biscuit/index:
-  - modules/nf-core/biscuit/index/**
-  - tests/modules/nf-core/biscuit/index/**
+- modules/nf-core/biscuit/index/**
+- tests/modules/nf-core/biscuit/index/**
 
 biscuit/mergecg:
-  - modules/nf-core/biscuit/index/**
-  - modules/nf-core/biscuit/mergecg/**
-  - tests/modules/nf-core/biscuit/mergecg/**
+- modules/nf-core/biscuit/index/**
+- modules/nf-core/biscuit/mergecg/**
+- tests/modules/nf-core/biscuit/mergecg/**
 
 biscuit/pileup:
-  - modules/nf-core/biscuit/index/**
-  - modules/nf-core/biscuit/pileup/**
-  - tests/modules/nf-core/biscuit/pileup/**
+- modules/nf-core/biscuit/index/**
+- modules/nf-core/biscuit/pileup/**
+- tests/modules/nf-core/biscuit/pileup/**
 
 biscuit/qc:
-  - modules/nf-core/biscuit/index/**
-  - modules/nf-core/biscuit/qc/**
-  - tests/modules/nf-core/biscuit/qc/**
+- modules/nf-core/biscuit/index/**
+- modules/nf-core/biscuit/qc/**
+- tests/modules/nf-core/biscuit/qc/**
 
 biscuit/vcf2bed:
-  - modules/nf-core/biscuit/vcf2bed/**
-  - tests/modules/nf-core/biscuit/vcf2bed/**
+- modules/nf-core/biscuit/vcf2bed/**
+- tests/modules/nf-core/biscuit/vcf2bed/**
 
 bismark/align:
-  - modules/nf-core/bismark/align/**
-  - modules/nf-core/bismark/genomepreparation/**
-  - tests/modules/nf-core/bismark/align/**
+- modules/nf-core/bismark/align/**
+- modules/nf-core/bismark/genomepreparation/**
+- tests/modules/nf-core/bismark/align/**
 
 bismark/deduplicate:
-  - modules/nf-core/bismark/deduplicate/**
-  - tests/modules/nf-core/bismark/deduplicate/**
+- modules/nf-core/bismark/deduplicate/**
+- tests/modules/nf-core/bismark/deduplicate/**
 
 bismark/genomepreparation:
-  - modules/nf-core/bismark/genomepreparation/**
-  - tests/modules/nf-core/bismark/genomepreparation/**
+- modules/nf-core/bismark/genomepreparation/**
+- tests/modules/nf-core/bismark/genomepreparation/**
 
 bismark/methylationextractor:
-  - modules/nf-core/bismark/methylationextractor/**
-  - modules/nf-core/bismark/genomepreparation/**
-  - tests/modules/nf-core/bismark/methylationextractor/**
+- modules/nf-core/bismark/methylationextractor/**
+- modules/nf-core/bismark/genomepreparation/**
+- tests/modules/nf-core/bismark/methylationextractor/**
 
 bismark/report:
-  - modules/nf-core/bismark/genomepreparation/**
-  - modules/nf-core/bismark/align/**
-  - modules/nf-core/bismark/deduplicate/**
-  - modules/nf-core/bismark/methylationextractor/**
-  - modules/nf-core/bismark/report/**
-  - tests/modules/nf-core/bismark/report/**
+- modules/nf-core/bismark/genomepreparation/**
+- modules/nf-core/bismark/align/**
+- modules/nf-core/bismark/deduplicate/**
+- modules/nf-core/bismark/methylationextractor/**
+- modules/nf-core/bismark/report/**
+- tests/modules/nf-core/bismark/report/**
 
 bismark/summary:
-  - modules/nf-core/bismark/genomepreparation/**
-  - modules/nf-core/bismark/align/**
-  - modules/nf-core/bismark/deduplicate/**
-  - modules/nf-core/bismark/methylationextractor/**
-  - modules/nf-core/bismark/summary/**
-  - tests/modules/nf-core/bismark/summary/**
+- modules/nf-core/bismark/genomepreparation/**
+- modules/nf-core/bismark/align/**
+- modules/nf-core/bismark/deduplicate/**
+- modules/nf-core/bismark/methylationextractor/**
+- modules/nf-core/bismark/summary/**
+- tests/modules/nf-core/bismark/summary/**
 
 blast/blastn:
-  - modules/nf-core/blast/blastn/**
-  - tests/modules/nf-core/blast/blastn/**
+- modules/nf-core/blast/blastn/**
+- tests/modules/nf-core/blast/blastn/**
 
 blast/makeblastdb:
-  - modules/nf-core/blast/makeblastdb/**
-  - tests/modules/nf-core/blast/makeblastdb/**
+- modules/nf-core/blast/makeblastdb/**
+- tests/modules/nf-core/blast/makeblastdb/**
 
 blast/tblastn:
-  - modules/nf-core/blast/tblastn/**
-  - tests/modules/nf-core/blast/tblastn/**
+- modules/nf-core/blast/tblastn/**
+- tests/modules/nf-core/blast/tblastn/**
 
 bowtie/align:
-  - modules/nf-core/bowtie/align/**
-  - modules/nf-core/bowtie/build/**
-  - tests/modules/nf-core/bowtie/align/**
+- modules/nf-core/bowtie/align/**
+- modules/nf-core/bowtie/build/**
+- tests/modules/nf-core/bowtie/align/**
 
 bowtie/build:
-  - modules/nf-core/bowtie/build/**
-  - tests/modules/nf-core/bowtie/build_test/**
+- modules/nf-core/bowtie/build/**
+- tests/modules/nf-core/bowtie/build_test/**
 
 bowtie2/align:
-  - modules/nf-core/bowtie2/align/**
-  - modules/nf-core/bowtie2/build/**
-  - tests/modules/nf-core/bowtie2/align/**
+- modules/nf-core/bowtie2/align/**
+- modules/nf-core/bowtie2/build/**
+- tests/modules/nf-core/bowtie2/align/**
 
 bowtie2/build:
-  - modules/nf-core/bowtie2/build/**
-  - tests/modules/nf-core/bowtie2/build_test/**
+- modules/nf-core/bowtie2/build/**
+- tests/modules/nf-core/bowtie2/build_test/**
 
 bracken/bracken:
-  - modules/nf-core/bracken/bracken/**
-  - tests/modules/nf-core/bracken/bracken/**
+- modules/nf-core/bracken/bracken/**
+- tests/modules/nf-core/bracken/bracken/**
 
 bracken/combinebrackenoutputs:
-  - modules/nf-core/bracken/combinebrackenoutputs/**
-  - tests/modules/nf-core/bracken/combinebrackenoutputs/**
+- modules/nf-core/bracken/combinebrackenoutputs/**
+- tests/modules/nf-core/bracken/combinebrackenoutputs/**
 
 busco:
-  - modules/nf-core/busco/**
-  - tests/modules/nf-core/busco/**
+- modules/nf-core/busco/**
+- tests/modules/nf-core/busco/**
 
 bwa/aln:
-  - modules/nf-core/bwa/aln/**
-  - tests/modules/nf-core/bwa/aln/**
+- modules/nf-core/bwa/aln/**
+- tests/modules/nf-core/bwa/aln/**
 
 bwa/index:
-  - modules/nf-core/bwa/index/**
-  - tests/modules/nf-core/bwa/index/**
+- modules/nf-core/bwa/index/**
+- tests/modules/nf-core/bwa/index/**
 
 bwa/mem:
-  - modules/nf-core/bwa/mem/**
-  - tests/modules/nf-core/bwa/mem/**
+- modules/nf-core/bwa/mem/**
+- tests/modules/nf-core/bwa/mem/**
 
 bwa/sampe:
-  - modules/nf-core/bwa/sampe/**
-  - tests/modules/nf-core/bwa/sampe/**
+- modules/nf-core/bwa/sampe/**
+- tests/modules/nf-core/bwa/sampe/**
 
 bwa/samse:
-  - modules/nf-core/bwa/samse/**
-  - tests/modules/nf-core/bwa/samse/**
+- modules/nf-core/bwa/samse/**
+- tests/modules/nf-core/bwa/samse/**
 
 bwamem2/index:
-  - modules/nf-core/bwamem2/index/**
-  - tests/modules/nf-core/bwamem2/index/**
+- modules/nf-core/bwamem2/index/**
+- tests/modules/nf-core/bwamem2/index/**
 
 bwamem2/mem:
-  - modules/nf-core/bwamem2/mem/**
-  - tests/modules/nf-core/bwamem2/mem/**
+- modules/nf-core/bwamem2/mem/**
+- tests/modules/nf-core/bwamem2/mem/**
 
 bwameth/align:
-  - modules/nf-core/bwameth/align/**
-  - tests/modules/nf-core/bwameth/align/**
+- modules/nf-core/bwameth/align/**
+- tests/modules/nf-core/bwameth/align/**
 
 bwameth/index:
-  - modules/nf-core/bwameth/index/**
-  - tests/modules/nf-core/bwameth/index/**
+- modules/nf-core/bwameth/index/**
+- tests/modules/nf-core/bwameth/index/**
 
 calder2:
-  - modules/nf-core/calder2/**
-  - tests/modules/nf-core/calder2/**
+- modules/nf-core/calder2/**
+- tests/modules/nf-core/calder2/**
 
 cat/cat:
-  - modules/nf-core/cat/cat/**
-  - tests/modules/nf-core/cat/cat/**
+- modules/nf-core/cat/cat/**
+- tests/modules/nf-core/cat/cat/**
 
 cat/fastq:
-  - modules/nf-core/cat/fastq/**
-  - tests/modules/nf-core/cat/fastq/**
+- modules/nf-core/cat/fastq/**
+- tests/modules/nf-core/cat/fastq/**
 
 cellranger/count:
-  - modules/nf-core/cellranger/count/**
-  - tests/modules/nf-core/cellranger/count/**
-  - modules/nf-core/cellranger/mkref/**
-  - tests/modules/nf-core/cellranger/mkref/**
-  - modules/nf-core/cellranger/gtf/**
-  - tests/modules/nf-core/cellranger/gtf/**
+- modules/nf-core/cellranger/count/**
+- tests/modules/nf-core/cellranger/count/**
+- modules/nf-core/cellranger/mkref/**
+- tests/modules/nf-core/cellranger/mkref/**
+- modules/nf-core/cellranger/gtf/**
+- tests/modules/nf-core/cellranger/gtf/**
 
 cellranger/gtf:
-  - modules/nf-core/cellranger/gtf/**
-  - tests/modules/nf-core/cellranger/gtf/**
+- modules/nf-core/cellranger/gtf/**
+- tests/modules/nf-core/cellranger/gtf/**
 
 cellranger/mkfastq:
-  - modules/nf-core/cellranger/mkfastq/**
-  - tests/modules/nf-core/cellranger/mkfastq/**
+- modules/nf-core/cellranger/mkfastq/**
+- tests/modules/nf-core/cellranger/mkfastq/**
 
 cellranger/mkgtf:
-  - modules/nf-core/cellranger/mkgtf/**
-  - tests/modules/nf-core/cellranger/mkgtf/**
+- modules/nf-core/cellranger/mkgtf/**
+- tests/modules/nf-core/cellranger/mkgtf/**
 
 cellranger/mkref:
-  - modules/nf-core/cellranger/mkref/**
-  - tests/modules/nf-core/cellranger/mkref/**
-  - modules/nf-core/cellranger/gtf/**
-  - tests/modules/nf-core/cellranger/gtf/**
+- modules/nf-core/cellranger/mkref/**
+- tests/modules/nf-core/cellranger/mkref/**
+- modules/nf-core/cellranger/gtf/**
+- tests/modules/nf-core/cellranger/gtf/**
 
 centrifuge/centrifuge:
-  - modules/nf-core/centrifuge/centrifuge/**
-  - tests/modules/nf-core/centrifuge/centrifuge/**
+- modules/nf-core/centrifuge/centrifuge/**
+- tests/modules/nf-core/centrifuge/centrifuge/**
 
 checkm/lineagewf:
-  - modules/nf-core/checkm/lineagewf/**
-  - tests/modules/nf-core/checkm/lineagewf/**
+- modules/nf-core/checkm/lineagewf/**
+- tests/modules/nf-core/checkm/lineagewf/**
 
 checkm/qa:
-  - modules/nf-core/checkm/qa/**
-  - tests/modules/nf-core/checkm/qa/**
+- modules/nf-core/checkm/qa/**
+- tests/modules/nf-core/checkm/qa/**
 
 chromap/chromap:
-  - modules/nf-core/chromap/chromap/**
-  - tests/modules/nf-core/chromap/chromap/**
+- modules/nf-core/chromap/chromap/**
+- tests/modules/nf-core/chromap/chromap/**
 
 chromap/index:
-  - modules/nf-core/chromap/index/**
-  - tests/modules/nf-core/chromap/index/**
+- modules/nf-core/chromap/index/**
+- tests/modules/nf-core/chromap/index/**
 
 circexplorer2/annotate:
-  - modules/nf-core/circexplorer2/annotate/**
-  - tests/modules/nf-core/circexplorer2/annotate/**
+- modules/nf-core/circexplorer2/annotate/**
+- tests/modules/nf-core/circexplorer2/annotate/**
 
 circexplorer2/parse:
-  - modules/nf-core/circexplorer2/parse/**
-  - tests/modules/nf-core/circexplorer2/parse/**
+- modules/nf-core/circexplorer2/parse/**
+- tests/modules/nf-core/circexplorer2/parse/**
 
 clonalframeml:
-  - modules/nf-core/clonalframeml/**
-  - tests/modules/nf-core/clonalframeml/**
+- modules/nf-core/clonalframeml/**
+- tests/modules/nf-core/clonalframeml/**
 
 cmseq/polymut:
-  - modules/nf-core/cmseq/polymut/**
-  - tests/modules/nf-core/cmseq/polymut/**
+- modules/nf-core/cmseq/polymut/**
+- tests/modules/nf-core/cmseq/polymut/**
 
 cnvkit/antitarget:
-  - modules/nf-core/cnvkit/antitarget/**
-  - tests/modules/nf-core/cnvkit/antitarget/**
+- modules/nf-core/cnvkit/antitarget/**
+- tests/modules/nf-core/cnvkit/antitarget/**
 
 cnvkit/batch:
-  - modules/nf-core/cnvkit/batch/**
-  - tests/modules/nf-core/cnvkit/batch/**
+- modules/nf-core/cnvkit/batch/**
+- tests/modules/nf-core/cnvkit/batch/**
 
 cnvkit/reference:
-  - modules/nf-core/cnvkit/reference/**
-  - tests/modules/nf-core/cnvkit/reference/**
+- modules/nf-core/cnvkit/reference/**
+- tests/modules/nf-core/cnvkit/reference/**
 
 concoct/concoct:
-  - modules/nf-core/concoct/concoct/**
-  - tests/modules/nf-core/concoct/concoct/**
+- modules/nf-core/concoct/concoct/**
+- tests/modules/nf-core/concoct/concoct/**
 
 concoct/concoctcoveragetable:
-  - modules/nf-core/concoct/concoctcoveragetable/**
-  - tests/modules/nf-core/concoct/concoctcoveragetable/**
+- modules/nf-core/concoct/concoctcoveragetable/**
+- tests/modules/nf-core/concoct/concoctcoveragetable/**
 
 concoct/cutupfasta:
-  - modules/nf-core/concoct/cutupfasta/**
-  - tests/modules/nf-core/concoct/cutupfasta/**
+- modules/nf-core/concoct/cutupfasta/**
+- tests/modules/nf-core/concoct/cutupfasta/**
 
 concoct/extractfastabins:
-  - modules/nf-core/concoct/extractfastabins/**
-  - tests/modules/nf-core/concoct/extractfastabins/**
+- modules/nf-core/concoct/extractfastabins/**
+- tests/modules/nf-core/concoct/extractfastabins/**
 
 concoct/mergecutupclustering:
-  - modules/nf-core/concoct/mergecutupclustering/**
-  - tests/modules/nf-core/concoct/mergecutupclustering/**
+- modules/nf-core/concoct/mergecutupclustering/**
+- tests/modules/nf-core/concoct/mergecutupclustering/**
 
 controlfreec/assesssignificance:
-  - modules/nf-core/controlfreec/assesssignificance/**
-  - tests/modules/nf-core/controlfreec/assesssignificance/**
+- modules/nf-core/controlfreec/assesssignificance/**
+- tests/modules/nf-core/controlfreec/assesssignificance/**
 
 controlfreec/freec:
-  - modules/nf-core/controlfreec/freec/**
-  - tests/modules/nf-core/controlfreec/freec/**
+- modules/nf-core/controlfreec/freec/**
+- tests/modules/nf-core/controlfreec/freec/**
 
 controlfreec/freec2bed:
-  - modules/nf-core/controlfreec/freec2bed/**
-  - tests/modules/nf-core/controlfreec/freec2bed/**
+- modules/nf-core/controlfreec/freec2bed/**
+- tests/modules/nf-core/controlfreec/freec2bed/**
 
 controlfreec/freec2circos:
-  - modules/nf-core/controlfreec/freec2circos/**
-  - tests/modules/nf-core/controlfreec/freec2circos/**
+- modules/nf-core/controlfreec/freec2circos/**
+- tests/modules/nf-core/controlfreec/freec2circos/**
 
 controlfreec/makegraph:
-  - modules/nf-core/controlfreec/makegraph/**
-  - tests/modules/nf-core/controlfreec/makegraph/**
+- modules/nf-core/controlfreec/makegraph/**
+- tests/modules/nf-core/controlfreec/makegraph/**
 
 cooler/cload:
-  - modules/nf-core/cooler/cload/**
-  - tests/modules/nf-core/cooler/cload/**
+- modules/nf-core/cooler/cload/**
+- tests/modules/nf-core/cooler/cload/**
 
 cooler/digest:
-  - modules/nf-core/cooler/digest/**
-  - tests/modules/nf-core/cooler/digest/**
+- modules/nf-core/cooler/digest/**
+- tests/modules/nf-core/cooler/digest/**
 
 cooler/dump:
-  - modules/nf-core/cooler/dump/**
-  - tests/modules/nf-core/cooler/dump/**
+- modules/nf-core/cooler/dump/**
+- tests/modules/nf-core/cooler/dump/**
 
 cooler/merge:
-  - modules/nf-core/cooler/merge/**
-  - tests/modules/nf-core/cooler/merge/**
+- modules/nf-core/cooler/merge/**
+- tests/modules/nf-core/cooler/merge/**
 
 cooler/zoomify:
-  - modules/nf-core/cooler/zoomify/**
-  - tests/software/cooler/zoomify/**
+- modules/nf-core/cooler/zoomify/**
+- tests/software/cooler/zoomify/**
 
 crumble:
-  - modules/nf-core/crumble/**
-  - tests/modules/nf-core/crumble/**
+- modules/nf-core/crumble/**
+- tests/modules/nf-core/crumble/**
 
 csvtk/concat:
-  - modules/nf-core/csvtk/concat/**
-  - tests/modules/nf-core/csvtk/concat/**
+- modules/nf-core/csvtk/concat/**
+- tests/modules/nf-core/csvtk/concat/**
 
 csvtk/split:
-  - modules/nf-core/csvtk/split/**
-  - tests/modules/nf-core/csvtk/split/**
+- modules/nf-core/csvtk/split/**
+- tests/modules/nf-core/csvtk/split/**
 
 custom/dumpsoftwareversions:
-  - modules/nf-core/custom/dumpsoftwareversions/**
-  - tests/modules/nf-core/custom/dumpsoftwareversions/**
+- modules/nf-core/custom/dumpsoftwareversions/**
+- tests/modules/nf-core/custom/dumpsoftwareversions/**
 
 custom/getchromsizes:
-  - modules/nf-core/custom/getchromsizes/**
-  - tests/modules/nf-core/custom/getchromsizes/**
+- modules/nf-core/custom/getchromsizes/**
+- tests/modules/nf-core/custom/getchromsizes/**
 
 custom/sratoolsncbisettings:
-  - modules/nf-core/custom/sratoolsncbisettings/**
-  - tests/modules/nf-core/custom/sratoolsncbisettings/**
+- modules/nf-core/custom/sratoolsncbisettings/**
+- tests/modules/nf-core/custom/sratoolsncbisettings/**
 
 cutadapt:
-  - modules/nf-core/cutadapt/**
-  - tests/modules/nf-core/cutadapt/**
+- modules/nf-core/cutadapt/**
+- tests/modules/nf-core/cutadapt/**
 
 damageprofiler:
-  - modules/nf-core/damageprofiler/**
-  - tests/modules/nf-core/damageprofiler/**
+- modules/nf-core/damageprofiler/**
+- tests/modules/nf-core/damageprofiler/**
 
 dastool/dastool:
-  - modules/nf-core/dastool/dastool/**
-  - tests/modules/nf-core/dastool/dastool/**
+- modules/nf-core/dastool/dastool/**
+- tests/modules/nf-core/dastool/dastool/**
 
 dastool/fastatocontig2bin:
-  - modules/nf-core/dastool/fastatocontig2bin/**
-  - tests/modules/nf-core/dastool/fastatocontig2bin/**
+- modules/nf-core/dastool/fastatocontig2bin/**
+- tests/modules/nf-core/dastool/fastatocontig2bin/**
 
 dastool/scaffolds2bin:
-  - modules/nf-core/dastool/scaffolds2bin/**
-  - tests/modules/nf-core/dastool/scaffolds2bin/**
+- modules/nf-core/dastool/scaffolds2bin/**
+- tests/modules/nf-core/dastool/scaffolds2bin/**
 
 dedup:
-  - modules/nf-core/dedup/**
-  - tests/modules/nf-core/dedup/**
+- modules/nf-core/dedup/**
+- tests/modules/nf-core/dedup/**
 
 deeparg/downloaddata:
-  - modules/nf-core/deeparg/downloaddata/**
-  - tests/modules/nf-core/deeparg/downloaddata/**
+- modules/nf-core/deeparg/downloaddata/**
+- tests/modules/nf-core/deeparg/downloaddata/**
 
 deeparg/predict:
-  - modules/nf-core/deeparg/predict/**
-  - tests/modules/nf-core/deeparg/predict/**
+- modules/nf-core/deeparg/predict/**
+- tests/modules/nf-core/deeparg/predict/**
 
 deepbgc/download:
-  - modules/nf-core/deepbgc/download/**
-  - tests/modules/nf-core/deepbgc/download/**
+- modules/nf-core/deepbgc/download/**
+- tests/modules/nf-core/deepbgc/download/**
 
 deepbgc/pipeline:
-  - modules/nf-core/deepbgc/pipeline/**
-  - tests/modules/nf-core/deepbgc/pipeline/**
+- modules/nf-core/deepbgc/pipeline/**
+- tests/modules/nf-core/deepbgc/pipeline/**
 
 deeptools/bamcoverage:
-  - modules/nf-core/deeptools/bamcoverage/**
-  - tests/modules/nf-core/deeptools/bamcoverage/**
+- modules/nf-core/deeptools/bamcoverage/**
+- tests/modules/nf-core/deeptools/bamcoverage/**
 
 deeptools/computematrix:
-  - modules/nf-core/deeptools/computematrix/**
-  - tests/modules/nf-core/deeptools/computematrix/**
+- modules/nf-core/deeptools/computematrix/**
+- tests/modules/nf-core/deeptools/computematrix/**
 
 deeptools/plotfingerprint:
-  - modules/nf-core/deeptools/plotfingerprint/**
-  - tests/modules/nf-core/deeptools/plotfingerprint/**
+- modules/nf-core/deeptools/plotfingerprint/**
+- tests/modules/nf-core/deeptools/plotfingerprint/**
 
 deeptools/plotheatmap:
-  - modules/nf-core/deeptools/plotheatmap/**
-  - tests/modules/nf-core/deeptools/plotheatmap/**
+- modules/nf-core/deeptools/plotheatmap/**
+- tests/modules/nf-core/deeptools/plotheatmap/**
 
 deeptools/plotprofile:
-  - modules/nf-core/deeptools/plotprofile/**
-  - tests/modules/nf-core/deeptools/plotprofile/**
+- modules/nf-core/deeptools/plotprofile/**
+- tests/modules/nf-core/deeptools/plotprofile/**
 
 deepvariant:
-  - modules/nf-core/deepvariant/**
-  - tests/modules/nf-core/deepvariant/**
+- modules/nf-core/deepvariant/**
+- tests/modules/nf-core/deepvariant/**
 
 delly/call:
-  - modules/nf-core/delly/call/**
-  - tests/modules/nf-core/delly/call/**
+- modules/nf-core/delly/call/**
+- tests/modules/nf-core/delly/call/**
 
 deseq2/differential:
-  - modules/nf-core/deseq2/differential/**
-  - tests/modules/nf-core/deseq2/differential/**
+- modules/nf-core/deseq2/differential/**
+- tests/modules/nf-core/deseq2/differential/**
 
 diamond/blastp:
-  - modules/nf-core/diamond/blastp/**
-  - tests/modules/nf-core/diamond/blastp/**
+- modules/nf-core/diamond/blastp/**
+- tests/modules/nf-core/diamond/blastp/**
 
 diamond/blastx:
-  - modules/nf-core/diamond/blastx/**
-  - tests/modules/nf-core/diamond/blastx/**
+- modules/nf-core/diamond/blastx/**
+- tests/modules/nf-core/diamond/blastx/**
 
 diamond/makedb:
-  - modules/nf-core/diamond/makedb/**
-  - tests/modules/nf-core/diamond/makedb/**
+- modules/nf-core/diamond/makedb/**
+- tests/modules/nf-core/diamond/makedb/**
 
 dragmap/align:
-  - modules/nf-core/dragmap/align/**
-  - tests/modules/nf-core/dragmap/align/**
+- modules/nf-core/dragmap/align/**
+- tests/modules/nf-core/dragmap/align/**
 
 dragmap/hashtable:
-  - modules/nf-core/dragmap/hashtable/**
-  - tests/modules/nf-core/dragmap/hashtable/**
+- modules/nf-core/dragmap/hashtable/**
+- tests/modules/nf-core/dragmap/hashtable/**
 
 dragonflye:
-  - modules/nf-core/dragonflye/**
-  - tests/modules/nf-core/dragonflye/**
+- modules/nf-core/dragonflye/**
+- tests/modules/nf-core/dragonflye/**
 
 dshbio/exportsegments:
-  - modules/nf-core/dshbio/exportsegments/**
-  - tests/modules/nf-core/dshbio/exportsegments/**
+- modules/nf-core/dshbio/exportsegments/**
+- tests/modules/nf-core/dshbio/exportsegments/**
 
 dshbio/filterbed:
-  - modules/nf-core/dshbio/filterbed/**
-  - tests/modules/nf-core/dshbio/filterbed/**
+- modules/nf-core/dshbio/filterbed/**
+- tests/modules/nf-core/dshbio/filterbed/**
 
 dshbio/filtergff3:
-  - modules/nf-core/dshbio/filtergff3/**
-  - tests/modules/nf-core/dshbio/filtergff3/**
+- modules/nf-core/dshbio/filtergff3/**
+- tests/modules/nf-core/dshbio/filtergff3/**
 
 dshbio/splitbed:
-  - modules/nf-core/dshbio/splitbed/**
-  - tests/modules/nf-core/dshbio/splitbed/**
+- modules/nf-core/dshbio/splitbed/**
+- tests/modules/nf-core/dshbio/splitbed/**
 
 dshbio/splitgff3:
-  - modules/nf-core/dshbio/splitgff3/**
-  - tests/modules/nf-core/dshbio/splitgff3/**
+- modules/nf-core/dshbio/splitgff3/**
+- tests/modules/nf-core/dshbio/splitgff3/**
 
 duphold:
-  - modules/nf-core/duphold/**
-  - tests/modules/nf-core/duphold/**
+- modules/nf-core/duphold/**
+- tests/modules/nf-core/duphold/**
 
 ectyper:
-  - modules/nf-core/ectyper/**
-  - tests/modules/nf-core/ectyper/**
+- modules/nf-core/ectyper/**
+- tests/modules/nf-core/ectyper/**
 
 eido/convert:
-  - modules/nf-core/eido/convert/**
-  - tests/modules/nf-core/eido/convert/**
+- modules/nf-core/eido/convert/**
+- tests/modules/nf-core/eido/convert/**
 
 eido/validate:
-  - modules/nf-core/eido/validate/**
-  - tests/modules/nf-core/eido/validate/**
+- modules/nf-core/eido/validate/**
+- tests/modules/nf-core/eido/validate/**
 
 elprep/filter:
-  - modules/nf-core/elprep/filter/**
-  - tests/modules/nf-core/elprep/filter/**
+- modules/nf-core/elprep/filter/**
+- tests/modules/nf-core/elprep/filter/**
 
 elprep/merge:
-  - modules/nf-core/elprep/merge/**
-  - tests/modules/nf-core/elprep/merge/**
+- modules/nf-core/elprep/merge/**
+- tests/modules/nf-core/elprep/merge/**
 
 elprep/split:
-  - modules/nf-core/elprep/split/**
-  - tests/modules/nf-core/elprep/split/**
+- modules/nf-core/elprep/split/**
+- tests/modules/nf-core/elprep/split/**
 
 emboss/seqret:
-  - modules/nf-core/emboss/seqret/**
-  - tests/modules/nf-core/emboss/seqret/**
+- modules/nf-core/emboss/seqret/**
+- tests/modules/nf-core/emboss/seqret/**
 
 emmtyper:
-  - modules/nf-core/emmtyper/**
-  - tests/modules/nf-core/emmtyper/**
+- modules/nf-core/emmtyper/**
+- tests/modules/nf-core/emmtyper/**
 
 endorspy:
-  - modules/nf-core/endorspy/**
-  - tests/modules/nf-core/endorspy/**
+- modules/nf-core/endorspy/**
+- tests/modules/nf-core/endorspy/**
 
 ensemblvep:
-  - modules/nf-core/ensemblvep/**
-  - tests/modules/nf-core/ensemblvep/**
+- modules/nf-core/ensemblvep/**
+- tests/modules/nf-core/ensemblvep/**
 
 entrezdirect/esearch:
-  - modules/nf-core/entrezdirect/esearch/**
-  - tests/modules/nf-core/entrezdirect/esearch/**
+- modules/nf-core/entrezdirect/esearch/**
+- tests/modules/nf-core/entrezdirect/esearch/**
 
 entrezdirect/esummary:
-  - modules/nf-core/entrezdirect/esummary/**
-  - tests/modules/nf-core/entrezdirect/esummary/**
+- modules/nf-core/entrezdirect/esummary/**
+- tests/modules/nf-core/entrezdirect/esummary/**
 
 entrezdirect/xtract:
-  - modules/nf-core/entrezdirect/xtract/**
-  - tests/modules/nf-core/entrezdirect/xtract/**
+- modules/nf-core/entrezdirect/xtract/**
+- tests/modules/nf-core/entrezdirect/xtract/**
 
 epang:
-  - modules/nf-core/epang/**
-  - tests/modules/nf-core/epang/
+- modules/nf-core/epang/**
+- tests/modules/nf-core/epang/
 
 expansionhunter:
-  - modules/nf-core/expansionhunter/**
-  - tests/modules/nf-core/expansionhunter/**
+- modules/nf-core/expansionhunter/**
+- tests/modules/nf-core/expansionhunter/**
 
 expansionhunterdenovo/merge:
-  - modules/nf-core/expansionhunterdenovo/merge/**
-  - tests/modules/nf-core/expansionhunterdenovo/merge/**
+- modules/nf-core/expansionhunterdenovo/merge/**
+- tests/modules/nf-core/expansionhunterdenovo/merge/**
 
 expansionhunterdenovo/profile:
-  - modules/nf-core/expansionhunterdenovo/profile/**
-  - tests/modules/nf-core/expansionhunterdenovo/profile/**
+- modules/nf-core/expansionhunterdenovo/profile/**
+- tests/modules/nf-core/expansionhunterdenovo/profile/**
 
 falco:
-  - modules/nf-core/falco/**
-  - tests/modules/nf-core/falco/**
+- modules/nf-core/falco/**
+- tests/modules/nf-core/falco/**
 
 faqcs:
-  - modules/nf-core/faqcs/**
-  - tests/modules/nf-core/faqcs/**
+- modules/nf-core/faqcs/**
+- tests/modules/nf-core/faqcs/**
 
 fargene:
-  - modules/nf-core/fargene/**
-  - tests/modules/nf-core/fargene/**
+- modules/nf-core/fargene/**
+- tests/modules/nf-core/fargene/**
 
 fastani:
-  - modules/nf-core/fastani/**
-  - tests/modules/nf-core/fastani/**
+- modules/nf-core/fastani/**
+- tests/modules/nf-core/fastani/**
 
 fastawindows:
-  - modules/nf-core/fastawindows/**
-  - tests/modules/nf-core/fastawindows/**
+- modules/nf-core/fastawindows/**
+- tests/modules/nf-core/fastawindows/**
 
 fastk/fastk:
-  - modules/nf-core/fastk/fastk/**
-  - tests/modules/nf-core/fastk/fastk/**
+- modules/nf-core/fastk/fastk/**
+- tests/modules/nf-core/fastk/fastk/**
 
 fastk/histex:
-  - modules/nf-core/fastk/histex/**
-  - tests/modules/nf-core/fastk/histex/**
+- modules/nf-core/fastk/histex/**
+- tests/modules/nf-core/fastk/histex/**
 
 fastk/merge:
-  - modules/nf-core/fastk/merge/**
-  - tests/modules/nf-core/fastk/merge/**
+- modules/nf-core/fastk/merge/**
+- tests/modules/nf-core/fastk/merge/**
 
 fastp:
-  - modules/nf-core/fastp/**
-  - tests/modules/nf-core/fastp/**
+- modules/nf-core/fastp/**
+- tests/modules/nf-core/fastp/**
 
 fastqc:
-  - modules/nf-core/fastqc/**
-  - tests/modules/nf-core/fastqc/**
+- modules/nf-core/fastqc/**
+- tests/modules/nf-core/fastqc/**
 
 fastqscan:
-  - modules/nf-core/fastqscan/**
-  - tests/modules/nf-core/fastqscan/**
+- modules/nf-core/fastqscan/**
+- tests/modules/nf-core/fastqscan/**
 
 fasttree:
-  - modules/nf-core/fasttree/**
-  - tests/modules/nf-core/fasttree/**
+- modules/nf-core/fasttree/**
+- tests/modules/nf-core/fasttree/**
 
 fcs/fcsadaptor:
-  - modules/nf-core/fcs/fcsadaptor/**
-  - tests/modules/nf-core/fcs/fcsadaptor/**
+- modules/nf-core/fcs/fcsadaptor/**
+- tests/modules/nf-core/fcs/fcsadaptor/**
 
 ffq:
-  - modules/nf-core/ffq/**
-  - tests/modules/nf-core/ffq/**
+- modules/nf-core/ffq/**
+- tests/modules/nf-core/ffq/**
 
 fgbio/callduplexconsensusreads:
-  - modules/nf-core/fgbio/callduplexconsensusreads/**
-  - tests/modules/nf-core/fgbio/callduplexconsensusreads/**
+- modules/nf-core/fgbio/callduplexconsensusreads/**
+- tests/modules/nf-core/fgbio/callduplexconsensusreads/**
 
 fgbio/callmolecularconsensusreads:
-  - modules/nf-core/fgbio/callmolecularconsensusreads/**
-  - tests/modules/nf-core/fgbio/callmolecularconsensusreads/**
+- modules/nf-core/fgbio/callmolecularconsensusreads/**
+- tests/modules/nf-core/fgbio/callmolecularconsensusreads/**
 
 fgbio/fastqtobam:
-  - modules/nf-core/fgbio/fastqtobam/**
-  - tests/modules/nf-core/fgbio/fastqtobam/**
+- modules/nf-core/fgbio/fastqtobam/**
+- tests/modules/nf-core/fgbio/fastqtobam/**
 
 fgbio/filterconsensusreads:
-  - modules/nf-core/fgbio/filterconsensusreads/**
-  - tests/modules/nf-core/fgbio/filterconsensusreads/**
+- modules/nf-core/fgbio/filterconsensusreads/**
+- tests/modules/nf-core/fgbio/filterconsensusreads/**
 
 fgbio/groupreadsbyumi:
-  - modules/nf-core/fgbio/groupreadsbyumi/**
-  - tests/modules/nf-core/fgbio/groupreadsbyumi/**
+- modules/nf-core/fgbio/groupreadsbyumi/**
+- tests/modules/nf-core/fgbio/groupreadsbyumi/**
 
 fgbio/sortbam:
-  - modules/nf-core/fgbio/sortbam/**
-  - tests/modules/nf-core/fgbio/sortbam/**
+- modules/nf-core/fgbio/sortbam/**
+- tests/modules/nf-core/fgbio/sortbam/**
 
 fgbio/zipperbams:
-  - modules/nf-core/fgbio/zipperbams/**
-  - tests/modules/nf-core/fgbio/zipperbams/**
+- modules/nf-core/fgbio/zipperbams/**
+- tests/modules/nf-core/fgbio/zipperbams/**
 
 filtlong:
-  - modules/nf-core/filtlong/**
-  - tests/modules/nf-core/filtlong/**
+- modules/nf-core/filtlong/**
+- tests/modules/nf-core/filtlong/**
 
 flash:
-  - modules/nf-core/flash/**
-  - tests/modules/nf-core/flash/**
+- modules/nf-core/flash/**
+- tests/modules/nf-core/flash/**
 
 flye:
-  - modules/nf-core/flye/**
-  - tests/modules/nf-core/flye/**
+- modules/nf-core/flye/**
+- tests/modules/nf-core/flye/**
 
 fq/lint:
-  - modules/nf-core/fq/lint/**
-  - tests/modules/nf-core/fq/lint/**
+- modules/nf-core/fq/lint/**
+- tests/modules/nf-core/fq/lint/**
 
 freebayes:
-  - modules/nf-core/freebayes/**
-  - tests/modules/nf-core/freebayes/**
+- modules/nf-core/freebayes/**
+- tests/modules/nf-core/freebayes/**
 
 gamma/gamma:
-  - modules/nf-core/gamma/gamma/**
-  - tests/modules/nf-core/gamma/gamma/**
+- modules/nf-core/gamma/gamma/**
+- tests/modules/nf-core/gamma/gamma/**
 
 gangstr:
-  - modules/nf-core/gangstr/**
-  - tests/modules/nf-core/gangstr/**
+- modules/nf-core/gangstr/**
+- tests/modules/nf-core/gangstr/**
 
 gappa/examineassign:
-  - modules/nf-core/gappa/examineassign/**
-  - tests/modules/nf-core/gappa/examineassign/**
+- modules/nf-core/gappa/examineassign/**
+- tests/modules/nf-core/gappa/examineassign/**
 
 gappa/examinegraft:
-  - modules/nf-core/gappa/examinegraft/**
-  - tests/modules/nf-core/gappa/examinegraft/**
+- modules/nf-core/gappa/examinegraft/**
+- tests/modules/nf-core/gappa/examinegraft/**
 
 gappa/examineheattree:
-  - modules/nf-core/gappa/examineheattree/**
-  - tests/modules/nf-core/gappa/examineheattree/**
+- modules/nf-core/gappa/examineheattree/**
+- tests/modules/nf-core/gappa/examineheattree/**
 
 gatk/indelrealigner:
-  - modules/nf-core/gatk/indelrealigner/**
-  - tests/modules/nf-core/gatk/indelrealigner/**
+- modules/nf-core/gatk/indelrealigner/**
+- tests/modules/nf-core/gatk/indelrealigner/**
 
 gatk/realignertargetcreator:
-  - modules/nf-core/gatk/realignertargetcreator/**
-  - tests/modules/nf-core/gatk/realignertargetcreator/**
+- modules/nf-core/gatk/realignertargetcreator/**
+- tests/modules/nf-core/gatk/realignertargetcreator/**
 
 gatk/unifiedgenotyper:
-  - modules/nf-core/gatk/unifiedgenotyper/**
-  - tests/modules/nf-core/gatk/unifiedgenotyper/**
+- modules/nf-core/gatk/unifiedgenotyper/**
+- tests/modules/nf-core/gatk/unifiedgenotyper/**
 
 gatk4/applybqsr:
-  - modules/nf-core/gatk4/applybqsr/**
-  - tests/modules/nf-core/gatk4/applybqsr/**
+- modules/nf-core/gatk4/applybqsr/**
+- tests/modules/nf-core/gatk4/applybqsr/**
 
 gatk4/applybqsrspark:
-  - modules/nf-core/gatk4/applybqsrspark/**
-  - tests/modules/nf-core/gatk4/applybqsrspark/**
+- modules/nf-core/gatk4/applybqsrspark/**
+- tests/modules/nf-core/gatk4/applybqsrspark/**
 
 gatk4/applyvqsr:
-  - modules/nf-core/gatk4/applyvqsr/**
-  - tests/modules/nf-core/gatk4/applyvqsr/**
+- modules/nf-core/gatk4/applyvqsr/**
+- tests/modules/nf-core/gatk4/applyvqsr/**
 
 gatk4/baserecalibrator:
-  - modules/nf-core/gatk4/baserecalibrator/**
-  - tests/modules/nf-core/gatk4/baserecalibrator/**
+- modules/nf-core/gatk4/baserecalibrator/**
+- tests/modules/nf-core/gatk4/baserecalibrator/**
 
 gatk4/baserecalibratorspark:
-  - modules/nf-core/gatk4/baserecalibratorspark/**
-  - tests/modules/nf-core/gatk4/baserecalibratorspark/**
+- modules/nf-core/gatk4/baserecalibratorspark/**
+- tests/modules/nf-core/gatk4/baserecalibratorspark/**
 
 gatk4/bedtointervallist:
-  - modules/nf-core/gatk4/bedtointervallist/**
-  - tests/modules/nf-core/gatk4/bedtointervallist/**
+- modules/nf-core/gatk4/bedtointervallist/**
+- tests/modules/nf-core/gatk4/bedtointervallist/**
 
 gatk4/calculatecontamination:
-  - modules/nf-core/gatk4/calculatecontamination/**
-  - tests/modules/nf-core/gatk4/calculatecontamination/**
+- modules/nf-core/gatk4/calculatecontamination/**
+- tests/modules/nf-core/gatk4/calculatecontamination/**
 
 gatk4/calibratedragstrmodel:
-  - modules/nf-core/gatk4/calibratedragstrmodel/**
-  - tests/modules/nf-core/gatk4/calibratedragstrmodel/**
+- modules/nf-core/gatk4/calibratedragstrmodel/**
+- tests/modules/nf-core/gatk4/calibratedragstrmodel/**
 
 gatk4/cnnscorevariants:
-  - modules/nf-core/gatk4/cnnscorevariants/**
-  - tests/modules/nf-core/gatk4/cnnscorevariants/**
+- modules/nf-core/gatk4/cnnscorevariants/**
+- tests/modules/nf-core/gatk4/cnnscorevariants/**
 
 gatk4/collectreadcounts:
-  - modules/nf-core/gatk4/collectreadcounts/**
-  - tests/modules/nf-core/gatk4/collectreadcounts/**
+- modules/nf-core/gatk4/collectreadcounts/**
+- tests/modules/nf-core/gatk4/collectreadcounts/**
 
 gatk4/collectsvevidence:
-  - modules/nf-core/gatk4/collectsvevidence/**
-  - tests/modules/nf-core/gatk4/collectsvevidence/**
+- modules/nf-core/gatk4/collectsvevidence/**
+- tests/modules/nf-core/gatk4/collectsvevidence/**
 
 gatk4/combinegvcfs:
-  - modules/nf-core/gatk4/combinegvcfs/**
-  - tests/modules/nf-core/gatk4/combinegvcfs/**
+- modules/nf-core/gatk4/combinegvcfs/**
+- tests/modules/nf-core/gatk4/combinegvcfs/**
 
 gatk4/composestrtablefile:
-  - modules/nf-core/gatk4/composestrtablefile/**
-  - tests/modules/nf-core/gatk4/composestrtablefile/**
+- modules/nf-core/gatk4/composestrtablefile/**
+- tests/modules/nf-core/gatk4/composestrtablefile/**
 
 gatk4/condensedepthevidence:
-  - modules/nf-core/gatk4/condensedepthevidence/**
-  - tests/modules/nf-core/gatk4/condensedepthevidence/**
+- modules/nf-core/gatk4/condensedepthevidence/**
+- tests/modules/nf-core/gatk4/condensedepthevidence/**
 
 gatk4/createsequencedictionary:
-  - modules/nf-core/gatk4/createsequencedictionary/**
-  - tests/modules/nf-core/gatk4/createsequencedictionary/**
+- modules/nf-core/gatk4/createsequencedictionary/**
+- tests/modules/nf-core/gatk4/createsequencedictionary/**
 
 gatk4/createsomaticpanelofnormals:
-  - modules/nf-core/gatk4/createsomaticpanelofnormals/**
-  - tests/modules/nf-core/gatk4/createsomaticpanelofnormals/**
+- modules/nf-core/gatk4/createsomaticpanelofnormals/**
+- tests/modules/nf-core/gatk4/createsomaticpanelofnormals/**
 
 gatk4/estimatelibrarycomplexity:
-  - modules/nf-core/gatk4/estimatelibrarycomplexity/**
-  - tests/modules/nf-core/gatk4/estimatelibrarycomplexity/**
+- modules/nf-core/gatk4/estimatelibrarycomplexity/**
+- tests/modules/nf-core/gatk4/estimatelibrarycomplexity/**
 
 gatk4/fastqtosam:
-  - modules/nf-core/gatk4/fastqtosam/**
-  - tests/modules/nf-core/gatk4/fastqtosam/**
+- modules/nf-core/gatk4/fastqtosam/**
+- tests/modules/nf-core/gatk4/fastqtosam/**
 
 gatk4/filtermutectcalls:
-  - modules/nf-core/gatk4/filtermutectcalls/**
-  - tests/modules/nf-core/gatk4/filtermutectcalls/**
+- modules/nf-core/gatk4/filtermutectcalls/**
+- tests/modules/nf-core/gatk4/filtermutectcalls/**
 
 gatk4/filtervarianttranches:
-  - modules/nf-core/gatk4/filtervarianttranches/**
-  - tests/modules/nf-core/gatk4/filtervarianttranches/**
+- modules/nf-core/gatk4/filtervarianttranches/**
+- tests/modules/nf-core/gatk4/filtervarianttranches/**
 
 gatk4/gatherbqsrreports:
-  - modules/nf-core/gatk4/gatherbqsrreports/**
-  - tests/modules/nf-core/gatk4/gatherbqsrreports/**
+- modules/nf-core/gatk4/gatherbqsrreports/**
+- tests/modules/nf-core/gatk4/gatherbqsrreports/**
 
 gatk4/gatherpileupsummaries:
-  - modules/nf-core/gatk4/gatherpileupsummaries/**
-  - tests/modules/nf-core/gatk4/gatherpileupsummaries/**
+- modules/nf-core/gatk4/gatherpileupsummaries/**
+- tests/modules/nf-core/gatk4/gatherpileupsummaries/**
 
 gatk4/genomicsdbimport:
-  - modules/nf-core/gatk4/genomicsdbimport/**
-  - tests/modules/nf-core/gatk4/genomicsdbimport/**
+- modules/nf-core/gatk4/genomicsdbimport/**
+- tests/modules/nf-core/gatk4/genomicsdbimport/**
 
 gatk4/genotypegvcfs:
-  - modules/nf-core/gatk4/genotypegvcfs/**
-  - tests/modules/nf-core/gatk4/genotypegvcfs/**
+- modules/nf-core/gatk4/genotypegvcfs/**
+- tests/modules/nf-core/gatk4/genotypegvcfs/**
 
 gatk4/getpileupsummaries:
-  - modules/nf-core/gatk4/getpileupsummaries/**
-  - tests/modules/nf-core/gatk4/getpileupsummaries/**
+- modules/nf-core/gatk4/getpileupsummaries/**
+- tests/modules/nf-core/gatk4/getpileupsummaries/**
 
 gatk4/haplotypecaller:
-  - modules/nf-core/gatk4/haplotypecaller/**
-  - tests/modules/nf-core/gatk4/haplotypecaller/**
+- modules/nf-core/gatk4/haplotypecaller/**
+- tests/modules/nf-core/gatk4/haplotypecaller/**
 
 gatk4/indexfeaturefile:
-  - modules/nf-core/gatk4/indexfeaturefile/**
-  - tests/modules/nf-core/gatk4/indexfeaturefile/**
+- modules/nf-core/gatk4/indexfeaturefile/**
+- tests/modules/nf-core/gatk4/indexfeaturefile/**
 
 gatk4/intervallisttobed:
-  - modules/nf-core/gatk4/intervallisttobed/**
-  - tests/modules/nf-core/gatk4/intervallisttobed/**
+- modules/nf-core/gatk4/intervallisttobed/**
+- tests/modules/nf-core/gatk4/intervallisttobed/**
 
 gatk4/intervallisttools:
-  - modules/nf-core/gatk4/intervallisttools/**
-  - tests/modules/nf-core/gatk4/intervallisttools/**
+- modules/nf-core/gatk4/intervallisttools/**
+- tests/modules/nf-core/gatk4/intervallisttools/**
 
 gatk4/learnreadorientationmodel:
-  - modules/nf-core/gatk4/learnreadorientationmodel/**
-  - tests/modules/nf-core/gatk4/learnreadorientationmodel/**
+- modules/nf-core/gatk4/learnreadorientationmodel/**
+- tests/modules/nf-core/gatk4/learnreadorientationmodel/**
 
 gatk4/leftalignandtrimvariants:
-  - modules/nf-core/gatk4/leftalignandtrimvariants/**
-  - tests/modules/nf-core/gatk4/leftalignandtrimvariants/**
+- modules/nf-core/gatk4/leftalignandtrimvariants/**
+- tests/modules/nf-core/gatk4/leftalignandtrimvariants/**
 
 gatk4/markduplicates:
-  - modules/nf-core/gatk4/markduplicates/**
-  - tests/modules/nf-core/gatk4/markduplicates/**
+- modules/nf-core/gatk4/markduplicates/**
+- tests/modules/nf-core/gatk4/markduplicates/**
 
 gatk4/markduplicatesspark:
-  - modules/nf-core/gatk4/markduplicatesspark/**
-  - tests/modules/nf-core/gatk4/markduplicatesspark/**
+- modules/nf-core/gatk4/markduplicatesspark/**
+- tests/modules/nf-core/gatk4/markduplicatesspark/**
 
 gatk4/mergebamalignment:
-  - modules/nf-core/gatk4/mergebamalignment/**
-  - tests/modules/nf-core/gatk4/mergebamalignment/**
+- modules/nf-core/gatk4/mergebamalignment/**
+- tests/modules/nf-core/gatk4/mergebamalignment/**
 
 gatk4/mergemutectstats:
-  - modules/nf-core/gatk4/mergemutectstats/**
-  - tests/modules/nf-core/gatk4/mergemutectstats/**
+- modules/nf-core/gatk4/mergemutectstats/**
+- tests/modules/nf-core/gatk4/mergemutectstats/**
 
 gatk4/mergevcfs:
-  - modules/nf-core/gatk4/mergevcfs/**
-  - tests/modules/nf-core/gatk4/mergevcfs/**
+- modules/nf-core/gatk4/mergevcfs/**
+- tests/modules/nf-core/gatk4/mergevcfs/**
 
 gatk4/mutect2:
-  - modules/nf-core/gatk4/mutect2/**
-  - tests/modules/nf-core/gatk4/mutect2/**
+- modules/nf-core/gatk4/mutect2/**
+- tests/modules/nf-core/gatk4/mutect2/**
 
 gatk4/printsvevidence:
-  - modules/nf-core/gatk4/printsvevidence/**
-  - tests/modules/nf-core/gatk4/printsvevidence/**
+- modules/nf-core/gatk4/printsvevidence/**
+- tests/modules/nf-core/gatk4/printsvevidence/**
 
 gatk4/reblockgvcf:
-  - modules/nf-core/gatk4/reblockgvcf/**
-  - tests/modules/nf-core/gatk4/reblockgvcf/**
+- modules/nf-core/gatk4/reblockgvcf/**
+- tests/modules/nf-core/gatk4/reblockgvcf/**
 
 gatk4/revertsam:
-  - modules/nf-core/gatk4/revertsam/**
-  - tests/modules/nf-core/gatk4/revertsam/**
+- modules/nf-core/gatk4/revertsam/**
+- tests/modules/nf-core/gatk4/revertsam/**
 
 gatk4/samtofastq:
-  - modules/nf-core/gatk4/samtofastq/**
-  - tests/modules/nf-core/gatk4/samtofastq/**
+- modules/nf-core/gatk4/samtofastq/**
+- tests/modules/nf-core/gatk4/samtofastq/**
 
 gatk4/selectvariants:
-  - modules/nf-core/gatk4/selectvariants/**
-  - tests/modules/nf-core/gatk4/selectvariants/**
+- modules/nf-core/gatk4/selectvariants/**
+- tests/modules/nf-core/gatk4/selectvariants/**
 
 gatk4/shiftfasta:
-  - modules/nf-core/gatk4/shiftfasta/**
-  - tests/modules/nf-core/gatk4/shiftfasta/**
+- modules/nf-core/gatk4/shiftfasta/**
+- tests/modules/nf-core/gatk4/shiftfasta/**
 
 gatk4/sitedepthtobaf:
-  - modules/nf-core/gatk4/sitedepthtobaf/**
-  - tests/modules/nf-core/gatk4/sitedepthtobaf/**
+- modules/nf-core/gatk4/sitedepthtobaf/**
+- tests/modules/nf-core/gatk4/sitedepthtobaf/**
 
 gatk4/splitintervals:
-  - modules/nf-core/gatk4/splitintervals/**
-  - tests/modules/nf-core/gatk4/splitintervals/**
+- modules/nf-core/gatk4/splitintervals/**
+- tests/modules/nf-core/gatk4/splitintervals/**
 
 gatk4/splitncigarreads:
-  - modules/nf-core/gatk4/splitncigarreads/**
-  - tests/modules/nf-core/gatk4/splitncigarreads/**
+- modules/nf-core/gatk4/splitncigarreads/**
+- tests/modules/nf-core/gatk4/splitncigarreads/**
 
 gatk4/svannotate:
-  - modules/nf-core/gatk4/svannotate/**
-  - tests/modules/nf-core/gatk4/svannotate/**
+- modules/nf-core/gatk4/svannotate/**
+- tests/modules/nf-core/gatk4/svannotate/**
 
 gatk4/svcluster:
-  - modules/nf-core/gatk4/svcluster/**
-  - tests/modules/nf-core/gatk4/svcluster/**
+- modules/nf-core/gatk4/svcluster/**
+- tests/modules/nf-core/gatk4/svcluster/**
 
 gatk4/variantfiltration:
-  - modules/nf-core/gatk4/variantfiltration/**
-  - tests/modules/nf-core/gatk4/variantfiltration/**
+- modules/nf-core/gatk4/variantfiltration/**
+- tests/modules/nf-core/gatk4/variantfiltration/**
 
 gatk4/variantrecalibrator:
-  - modules/nf-core/gatk4/variantrecalibrator/**
-  - tests/modules/nf-core/gatk4/variantrecalibrator/**
+- modules/nf-core/gatk4/variantrecalibrator/**
+- tests/modules/nf-core/gatk4/variantrecalibrator/**
 
 gecco/run:
-  - modules/nf-core/gecco/run/**
-  - tests/modules/nf-core/gecco/run/**
+- modules/nf-core/gecco/run/**
+- tests/modules/nf-core/gecco/run/**
 
 genescopefk:
-  - modules/nf-core/genescopefk/**
-  - tests/modules/nf-core/genescopefk/**
+- modules/nf-core/genescopefk/**
+- tests/modules/nf-core/genescopefk/**
 
 genmap/index:
-  - modules/nf-core/genmap/index/**
-  - tests/modules/nf-core/genmap/index/**
+- modules/nf-core/genmap/index/**
+- tests/modules/nf-core/genmap/index/**
 
 genmap/mappability:
-  - modules/nf-core/genmap/mappability/**
-  - tests/modules/nf-core/genmap/mappability/**
+- modules/nf-core/genmap/mappability/**
+- tests/modules/nf-core/genmap/mappability/**
 
 genmod/annotate:
-  - modules/nf-core/genmod/annotate/**
-  - tests/modules/nf-core/genmod/annotate/**
+- modules/nf-core/genmod/annotate/**
+- tests/modules/nf-core/genmod/annotate/**
 
 genmod/compound:
-  - modules/nf-core/genmod/compound/**
-  - tests/modules/nf-core/genmod/compound/**
+- modules/nf-core/genmod/compound/**
+- tests/modules/nf-core/genmod/compound/**
 
 genmod/models:
-  - modules/nf-core/genmod/models/**
-  - tests/modules/nf-core/genmod/models/**
+- modules/nf-core/genmod/models/**
+- tests/modules/nf-core/genmod/models/**
 
 genmod/score:
-  - modules/nf-core/genmod/score/**
-  - tests/modules/nf-core/genmod/score/**
+- modules/nf-core/genmod/score/**
+- tests/modules/nf-core/genmod/score/**
 
 genomescope2:
-  - modules/nf-core/genomescope2/**
-  - tests/modules/nf-core/genomescope2/**
+- modules/nf-core/genomescope2/**
+- tests/modules/nf-core/genomescope2/**
 
 genotyphi/parse:
-  - modules/nf-core/genotyphi/parse/**
-  - tests/modules/nf-core/genotyphi/parse/**
+- modules/nf-core/genotyphi/parse/**
+- tests/modules/nf-core/genotyphi/parse/**
 
 genrich:
-  - modules/nf-core/genrich/**
-  - tests/modules/nf-core/genrich/**
+- modules/nf-core/genrich/**
+- tests/modules/nf-core/genrich/**
 
 gfaffix:
-  - modules/nf-core/gfaffix/**
-  - tests/modules/nf-core/gfaffix/**
+- modules/nf-core/gfaffix/**
+- tests/modules/nf-core/gfaffix/**
 
 gffread:
-  - modules/nf-core/gffread/**
-  - tests/modules/nf-core/gffread/**
+- modules/nf-core/gffread/**
+- tests/modules/nf-core/gffread/**
 
 glimpse/chunk:
-  - modules/nf-core/glimpse/chunk/**
-  - tests/modules/nf-core/glimpse/chunk/**
+- modules/nf-core/glimpse/chunk/**
+- tests/modules/nf-core/glimpse/chunk/**
 
 glnexus:
-  - modules/nf-core/glnexus/**
-  - tests/modules/nf-core/glnexus/**
+- modules/nf-core/glnexus/**
+- tests/modules/nf-core/glnexus/**
 
 goat/taxonsearch:
-  - modules/nf-core/goat/taxonsearch/**
-  - tests/modules/nf-core/goat/taxonsearch/**
+- modules/nf-core/goat/taxonsearch/**
+- tests/modules/nf-core/goat/taxonsearch/**
 
 graphmap2/align:
-  - modules/nf-core/graphmap2/align/**
-  - tests/modules/nf-core/graphmap2/align/**
+- modules/nf-core/graphmap2/align/**
+- tests/modules/nf-core/graphmap2/align/**
 
 graphmap2/index:
-  - modules/nf-core/graphmap2/index/**
-  - tests/modules/nf-core/graphmap2/index/**
+- modules/nf-core/graphmap2/index/**
+- tests/modules/nf-core/graphmap2/index/**
 
 gstama/collapse:
-  - modules/nf-core/gstama/collapse/**
-  - tests/modules/nf-core/gstama/collapse/**
+- modules/nf-core/gstama/collapse/**
+- tests/modules/nf-core/gstama/collapse/**
 
 gstama/merge:
-  - modules/nf-core/gstama/merge/**
-  - tests/modules/nf-core/gstama/merge/**
+- modules/nf-core/gstama/merge/**
+- tests/modules/nf-core/gstama/merge/**
 
 gstama/polyacleanup:
-  - modules/nf-core/gstama/polyacleanup/**
-  - tests/modules/nf-core/gstama/polyacleanup/**
+- modules/nf-core/gstama/polyacleanup/**
+- tests/modules/nf-core/gstama/polyacleanup/**
 
 gtdbtk/classifywf:
-  - modules/nf-core/gtdbtk/classifywf/**
-  - tests/modules/nf-core/gtdbtk/classifywf/**
+- modules/nf-core/gtdbtk/classifywf/**
+- tests/modules/nf-core/gtdbtk/classifywf/**
 
 gubbins:
-  - modules/nf-core/gubbins/**
-  - tests/modules/nf-core/gubbins/**
+- modules/nf-core/gubbins/**
+- tests/modules/nf-core/gubbins/**
 
 gunc/downloaddb:
-  - modules/nf-core/gunc/downloaddb/**
-  - tests/modules/nf-core/gunc/downloaddb/**
+- modules/nf-core/gunc/downloaddb/**
+- tests/modules/nf-core/gunc/downloaddb/**
 
 gunc/run:
-  - modules/nf-core/gunc/run/**
-  - tests/modules/nf-core/gunc/run/**
+- modules/nf-core/gunc/run/**
+- tests/modules/nf-core/gunc/run/**
 
 gunzip:
-  - modules/nf-core/gunzip/**
-  - tests/modules/nf-core/gunzip/**
+- modules/nf-core/gunzip/**
+- tests/modules/nf-core/gunzip/**
 
 gvcftools/extractvariants:
-  - modules/nf-core/gvcftools/extractvariants/**
-  - tests/modules/nf-core/gvcftools/extractvariants/**
+- modules/nf-core/gvcftools/extractvariants/**
+- tests/modules/nf-core/gvcftools/extractvariants/**
 
 hamronization/abricate:
-  - modules/nf-core/hamronization/abricate/**
-  - tests/modules/nf-core/hamronization/abricate/**
+- modules/nf-core/hamronization/abricate/**
+- tests/modules/nf-core/hamronization/abricate/**
 
 hamronization/amrfinderplus:
-  - modules/nf-core/hamronization/amrfinderplus/**
-  - tests/modules/nf-core/hamronization/amrfinderplus/**
+- modules/nf-core/hamronization/amrfinderplus/**
+- tests/modules/nf-core/hamronization/amrfinderplus/**
 
 hamronization/deeparg:
-  - modules/nf-core/hamronization/deeparg/**
-  - tests/modules/nf-core/hamronization/deeparg/**
+- modules/nf-core/hamronization/deeparg/**
+- tests/modules/nf-core/hamronization/deeparg/**
 
 hamronization/fargene:
-  - modules/nf-core/hamronization/fargene/**
-  - tests/modules/nf-core/hamronization/fargene/**
+- modules/nf-core/hamronization/fargene/**
+- tests/modules/nf-core/hamronization/fargene/**
 
 hamronization/rgi:
-  - modules/nf-core/hamronization/rgi/**
-  - tests/modules/nf-core/hamronization/rgi/**
+- modules/nf-core/hamronization/rgi/**
+- tests/modules/nf-core/hamronization/rgi/**
 
 hamronization/summarize:
-  - modules/nf-core/hamronization/summarize/**
-  - tests/modules/nf-core/hamronization/summarize/**
+- modules/nf-core/hamronization/summarize/**
+- tests/modules/nf-core/hamronization/summarize/**
 
 hapibd:
-  - modules/nf-core/hapibd/**
-  - tests/modules/nf-core/hapibd/**
+- modules/nf-core/hapibd/**
+- tests/modules/nf-core/hapibd/**
 
 haplocheck:
-  - modules/nf-core/haplocheck/**
-  - tests/modules/nf-core/haplocheck/**
+- modules/nf-core/haplocheck/**
+- tests/modules/nf-core/haplocheck/**
 
 haplogrep2/classify:
-  - modules/nf-core/haplogrep2/classify/**
-  - tests/modules/nf-core/haplogrep2/classify/**
+- modules/nf-core/haplogrep2/classify/**
+- tests/modules/nf-core/haplogrep2/classify/**
 
 happy/happy:
-  - modules/nf-core/happy/happy/**
-  - tests/modules/nf-core/happy/happy/**
+- modules/nf-core/happy/happy/**
+- tests/modules/nf-core/happy/happy/**
 
 happy/prepy:
-  - modules/nf-core/happy/prepy/**
-  - tests/modules/nf-core/happy/prepy/**
+- modules/nf-core/happy/prepy/**
+- tests/modules/nf-core/happy/prepy/**
 
 hicap:
-  - modules/nf-core/hicap/**
-  - tests/modules/nf-core/hicap/**
+- modules/nf-core/hicap/**
+- tests/modules/nf-core/hicap/**
 
 hifiasm:
-  - modules/nf-core/hifiasm/**
-  - tests/modules/nf-core/hifiasm/**
+- modules/nf-core/hifiasm/**
+- tests/modules/nf-core/hifiasm/**
 
 hisat2/align:
-  - modules/nf-core/hisat2/align/**
-  - modules/nf-core/hisat2/build/**
-  - modules/nf-core/hisat2/extractsplicesites/**
-  - tests/modules/nf-core/hisat2/align/**
+- modules/nf-core/hisat2/align/**
+- modules/nf-core/hisat2/build/**
+- modules/nf-core/hisat2/extractsplicesites/**
+- tests/modules/nf-core/hisat2/align/**
 
 hisat2/build:
-  - modules/nf-core/hisat2/build/**
-  - modules/nf-core/hisat2/extractsplicesites/**
-  - tests/modules/nf-core/hisat2/build_test/**
+- modules/nf-core/hisat2/build/**
+- modules/nf-core/hisat2/extractsplicesites/**
+- tests/modules/nf-core/hisat2/build_test/**
 
 hisat2/extractsplicesites:
-  - modules/nf-core/hisat2/extractsplicesites/**
-  - tests/modules/nf-core/hisat2/extractsplicesites/**
+- modules/nf-core/hisat2/extractsplicesites/**
+- tests/modules/nf-core/hisat2/extractsplicesites/**
 
 hmmcopy/gccounter:
-  - modules/nf-core/hmmcopy/gccounter/**
-  - tests/modules/nf-core/hmmcopy/gccounter/**
+- modules/nf-core/hmmcopy/gccounter/**
+- tests/modules/nf-core/hmmcopy/gccounter/**
 
 hmmcopy/generatemap:
-  - modules/nf-core/hmmcopy/generatemap/**
-  - tests/modules/nf-core/hmmcopy/generatemap/**
+- modules/nf-core/hmmcopy/generatemap/**
+- tests/modules/nf-core/hmmcopy/generatemap/**
 
 hmmcopy/mapcounter:
-  - modules/nf-core/hmmcopy/mapcounter/**
-  - tests/modules/nf-core/hmmcopy/mapcounter/**
+- modules/nf-core/hmmcopy/mapcounter/**
+- tests/modules/nf-core/hmmcopy/mapcounter/**
 
 hmmcopy/readcounter:
-  - modules/nf-core/hmmcopy/readcounter/**
-  - tests/modules/nf-core/hmmcopy/readcounter/**
+- modules/nf-core/hmmcopy/readcounter/**
+- tests/modules/nf-core/hmmcopy/readcounter/**
 
 hmmer/eslalimask:
-  - modules/nf-core/hmmer/eslalimask/**
-  - tests/modules/nf-core/hmmer/eslalimask/**
+- modules/nf-core/hmmer/eslalimask/**
+- tests/modules/nf-core/hmmer/eslalimask/**
 
 hmmer/eslreformat:
-  - modules/nf-core/hmmer/eslreformat/**
-  - tests/modules/nf-core/hmmer/eslreformat/**
+- modules/nf-core/hmmer/eslreformat/**
+- tests/modules/nf-core/hmmer/eslreformat/**
 
 hmmer/hmmalign:
-  - modules/nf-core/hmmer/hmmalign/**
-  - tests/modules/nf-core/hmmer/hmmalign/**
+- modules/nf-core/hmmer/hmmalign/**
+- tests/modules/nf-core/hmmer/hmmalign/**
 
 hmmer/hmmbuild:
-  - modules/nf-core/hmmer/hmmbuild/**
-  - tests/modules/nf-core/hmmer/hmmbuild/**
+- modules/nf-core/hmmer/hmmbuild/**
+- tests/modules/nf-core/hmmer/hmmbuild/**
 
 hmmer/hmmsearch:
-  - modules/nf-core/hmmer/hmmsearch/**
-  - tests/modules/nf-core/hmmer/hmmsearch/**
+- modules/nf-core/hmmer/hmmsearch/**
+- tests/modules/nf-core/hmmer/hmmsearch/**
 
 hmtnote:
-  - modules/nf-core/hmtnote/**
-  - tests/modules/nf-core/hmtnote/**
+- modules/nf-core/hmtnote/**
+- tests/modules/nf-core/hmtnote/**
 
 homer/annotatepeaks:
-  - modules/nf-core/homer/annotatepeaks/**
-  - tests/modules/nf-core/homer/annotatepeaks/**
+- modules/nf-core/homer/annotatepeaks/**
+- tests/modules/nf-core/homer/annotatepeaks/**
 
 homer/findpeaks:
-  - modules/nf-core/homer/findpeaks/**
-  - modules/nf-core/homer/maketagdirectory/**
-  - tests/modules/nf-core/homer/findpeaks/**
+- modules/nf-core/homer/findpeaks/**
+- modules/nf-core/homer/maketagdirectory/**
+- tests/modules/nf-core/homer/findpeaks/**
 
 homer/maketagdirectory:
-  - modules/nf-core/homer/maketagdirectory/**
-  - tests/modules/nf-core/homer/maketagdirectory/**
+- modules/nf-core/homer/maketagdirectory/**
+- tests/modules/nf-core/homer/maketagdirectory/**
 
 homer/makeucscfile:
-  - modules/nf-core/homer/makeucscfile/**
-  - tests/modules/nf-core/homer/makeucscfile/**
+- modules/nf-core/homer/makeucscfile/**
+- tests/modules/nf-core/homer/makeucscfile/**
 
 homer/pos2bed:
-  - modules/nf-core/homer/pos2bed/**
-  - modules/nf-core/homer/maketagdirectory/**
-  - modules/nf-core/homer/findpeaks/**
-  - tests/modules/nf-core/homer/pos2bed/**
+- modules/nf-core/homer/pos2bed/**
+- modules/nf-core/homer/maketagdirectory/**
+- modules/nf-core/homer/findpeaks/**
+- tests/modules/nf-core/homer/pos2bed/**
 
 hpsuissero:
-  - modules/nf-core/hpsuissero/**
-  - tests/modules/nf-core/hpsuissero/**
+- modules/nf-core/hpsuissero/**
+- tests/modules/nf-core/hpsuissero/**
 
 ichorcna/createpon:
-  - modules/nf-core/ichorcna/createpon/**
-  - tests/modules/nf-core/ichorcna/createpon/**
+- modules/nf-core/ichorcna/createpon/**
+- tests/modules/nf-core/ichorcna/createpon/**
 
 ichorcna/run:
-  - modules/nf-core/ichorcna/run/**
-  - tests/modules/nf-core/ichorcna/run/**
+- modules/nf-core/ichorcna/run/**
+- tests/modules/nf-core/ichorcna/run/**
 
 idr:
-  - modules/nf-core/idr/**
-  - tests/modules/nf-core/idr/**
+- modules/nf-core/idr/**
+- tests/modules/nf-core/idr/**
 
 imputeme/vcftoprs:
-  - modules/nf-core/imputeme/vcftoprs/**
-  - tests/modules/nf-core/imputeme/vcftoprs/**
+- modules/nf-core/imputeme/vcftoprs/**
+- tests/modules/nf-core/imputeme/vcftoprs/**
 
 instrain/profile:
-  - modules/nf-core/instrain/profile/**
-  - tests/modules/nf-core/instrain/profile/**
+- modules/nf-core/instrain/profile/**
+- tests/modules/nf-core/instrain/profile/**
 
 iqtree:
-  - modules/nf-core/iqtree/**
-  - tests/modules/nf-core/iqtree/**
+- modules/nf-core/iqtree/**
+- tests/modules/nf-core/iqtree/**
 
 ismapper:
-  - modules/nf-core/ismapper/**
-  - tests/modules/nf-core/ismapper/**
+- modules/nf-core/ismapper/**
+- tests/modules/nf-core/ismapper/**
 
 isoseq3/cluster:
-  - modules/nf-core/isoseq3/cluster/**
-  - tests/modules/nf-core/isoseq3/cluster/**
+- modules/nf-core/isoseq3/cluster/**
+- tests/modules/nf-core/isoseq3/cluster/**
 
 isoseq3/refine:
-  - modules/nf-core/isoseq3/refine/**
-  - tests/modules/nf-core/isoseq3/refine/**
+- modules/nf-core/isoseq3/refine/**
+- tests/modules/nf-core/isoseq3/refine/**
 
 ivar/consensus:
-  - modules/nf-core/ivar/consensus/**
-  - tests/modules/nf-core/ivar/consensus/**
+- modules/nf-core/ivar/consensus/**
+- tests/modules/nf-core/ivar/consensus/**
 
 ivar/trim:
-  - modules/nf-core/ivar/trim/**
-  - tests/modules/nf-core/ivar/trim/**
+- modules/nf-core/ivar/trim/**
+- tests/modules/nf-core/ivar/trim/**
 
 ivar/variants:
-  - modules/nf-core/ivar/variants/**
-  - tests/modules/nf-core/ivar/variants/**
+- modules/nf-core/ivar/variants/**
+- tests/modules/nf-core/ivar/variants/**
 
 jupyternotebook:
-  - modules/nf-core/jupyternotebook/**
-  - tests/modules/nf-core/jupyternotebook/**
+- modules/nf-core/jupyternotebook/**
+- tests/modules/nf-core/jupyternotebook/**
 
 kaiju/kaiju:
-  - modules/nf-core/kaiju/kaiju/**
-  - tests/modules/nf-core/kaiju/kaiju/**
+- modules/nf-core/kaiju/kaiju/**
+- tests/modules/nf-core/kaiju/kaiju/**
 
 kaiju/kaiju2krona:
-  - modules/nf-core/kaiju/kaiju2krona/**
-  - tests/modules/nf-core/kaiju/kaiju2krona/**
+- modules/nf-core/kaiju/kaiju2krona/**
+- tests/modules/nf-core/kaiju/kaiju2krona/**
 
 kaiju/kaiju2table:
-  - modules/nf-core/kaiju/kaiju2table/**
-  - tests/modules/nf-core/kaiju/kaiju2table/**
+- modules/nf-core/kaiju/kaiju2table/**
+- tests/modules/nf-core/kaiju/kaiju2table/**
 
 kallisto/index:
-  - modules/nf-core/kallisto/index/**
-  - tests/modules/nf-core/kallisto/index/**
+- modules/nf-core/kallisto/index/**
+- tests/modules/nf-core/kallisto/index/**
 
 kallistobustools/count:
-  - modules/nf-core/kallistobustools/count/**
-  - tests/modules/nf-core/kallistobustools/count/**
+- modules/nf-core/kallistobustools/count/**
+- tests/modules/nf-core/kallistobustools/count/**
 
 kallistobustools/ref:
-  - modules/nf-core/kallistobustools/ref/**
-  - tests/modules/nf-core/kallistobustools/ref/**
+- modules/nf-core/kallistobustools/ref/**
+- tests/modules/nf-core/kallistobustools/ref/**
 
 kat/hist:
-  - modules/nf-core/kat/hist/**
-  - tests/modules/nf-core/kat/hist/**
+- modules/nf-core/kat/hist/**
+- tests/modules/nf-core/kat/hist/**
 
 khmer/normalizebymedian:
-  - modules/nf-core/khmer/normalizebymedian/**
-  - tests/modules/nf-core/khmer/normalizebymedian/**
+- modules/nf-core/khmer/normalizebymedian/**
+- tests/modules/nf-core/khmer/normalizebymedian/**
 
 khmer/uniquekmers:
-  - modules/nf-core/khmer/uniquekmers/**
-  - tests/modules/nf-core/khmer/uniquekmers/**
+- modules/nf-core/khmer/uniquekmers/**
+- tests/modules/nf-core/khmer/uniquekmers/**
 
 kleborate:
-  - modules/nf-core/kleborate/**
-  - tests/modules/nf-core/kleborate/**
+- modules/nf-core/kleborate/**
+- tests/modules/nf-core/kleborate/**
 
 kofamscan:
-  - modules/nf-core/kofamscan/**
-  - tests/modules/nf-core/kofamscan/**
+- modules/nf-core/kofamscan/**
+- tests/modules/nf-core/kofamscan/**
 
 kraken2/kraken2:
-  - modules/nf-core/kraken2/kraken2/**
-  - modules/nf-core/untar/**
-  - tests/modules/nf-core/kraken2/kraken2/**
+- modules/nf-core/kraken2/kraken2/**
+- modules/nf-core/untar/**
+- tests/modules/nf-core/kraken2/kraken2/**
 
 krakentools/combinekreports:
-  - modules/nf-core/krakentools/combinekreports/**
-  - tests/modules/nf-core/krakentools/combinekreports/**
+- modules/nf-core/krakentools/combinekreports/**
+- tests/modules/nf-core/krakentools/combinekreports/**
 
 krakentools/kreport2krona:
-  - modules/nf-core/krakentools/kreport2krona/**
-  - tests/modules/nf-core/krakentools/kreport2krona/**
+- modules/nf-core/krakentools/kreport2krona/**
+- tests/modules/nf-core/krakentools/kreport2krona/**
 
 krakenuniq/build:
-  - modules/nf-core/krakenuniq/build/**
-  - tests/modules/nf-core/krakenuniq/build/**
+- modules/nf-core/krakenuniq/build/**
+- tests/modules/nf-core/krakenuniq/build/**
 
 krakenuniq/download:
-  - modules/nf-core/krakenuniq/download/**
-  - tests/modules/nf-core/krakenuniq/download/**
+- modules/nf-core/krakenuniq/download/**
+- tests/modules/nf-core/krakenuniq/download/**
 
 krakenuniq/preloadedkrakenuniq:
-  - modules/nf-core/krakenuniq/preloadedkrakenuniq/**
-  - tests/modules/nf-core/krakenuniq/preloadedkrakenuniq/**
+- modules/nf-core/krakenuniq/preloadedkrakenuniq/**
+- tests/modules/nf-core/krakenuniq/preloadedkrakenuniq/**
 
 krona/kronadb:
-  - modules/nf-core/krona/kronadb/**
-  - tests/modules/nf-core/krona/kronadb/**
+- modules/nf-core/krona/kronadb/**
+- tests/modules/nf-core/krona/kronadb/**
 
 krona/ktimporttaxonomy:
-  - modules/nf-core/krona/ktimporttaxonomy/**
-  - tests/modules/nf-core/krona/ktimporttaxonomy/**
+- modules/nf-core/krona/ktimporttaxonomy/**
+- tests/modules/nf-core/krona/ktimporttaxonomy/**
 
 krona/ktimporttext:
-  - modules/nf-core/krona/ktimporttext/**
-  - tests/modules/nf-core/krona/ktimporttext/**
+- modules/nf-core/krona/ktimporttext/**
+- tests/modules/nf-core/krona/ktimporttext/**
 
 krona/ktupdatetaxonomy:
-  - modules/nf-core/krona/ktupdatetaxonomy/**
-  - tests/modules/nf-core/krona/ktupdatetaxonomy/**
+- modules/nf-core/krona/ktupdatetaxonomy/**
+- tests/modules/nf-core/krona/ktupdatetaxonomy/**
 
 last/dotplot:
-  - modules/nf-core/last/dotplot/**
-  - tests/modules/nf-core/last/dotplot/**
+- modules/nf-core/last/dotplot/**
+- tests/modules/nf-core/last/dotplot/**
 
 last/lastal:
-  - modules/nf-core/last/lastal/**
-  - tests/modules/nf-core/last/lastal/**
+- modules/nf-core/last/lastal/**
+- tests/modules/nf-core/last/lastal/**
 
 last/lastdb:
-  - modules/nf-core/last/lastdb/**
-  - tests/modules/nf-core/last/lastdb/**
+- modules/nf-core/last/lastdb/**
+- tests/modules/nf-core/last/lastdb/**
 
 last/mafconvert:
-  - modules/nf-core/last/mafconvert/**
-  - tests/modules/nf-core/last/mafconvert/**
+- modules/nf-core/last/mafconvert/**
+- tests/modules/nf-core/last/mafconvert/**
 
 last/mafswap:
-  - modules/nf-core/last/mafswap/**
-  - tests/modules/nf-core/last/mafswap/**
+- modules/nf-core/last/mafswap/**
+- tests/modules/nf-core/last/mafswap/**
 
 last/postmask:
-  - modules/nf-core/last/postmask/**
-  - tests/modules/nf-core/last/postmask/**
+- modules/nf-core/last/postmask/**
+- tests/modules/nf-core/last/postmask/**
 
 last/split:
-  - modules/nf-core/last/split/**
-  - tests/modules/nf-core/last/split/**
+- modules/nf-core/last/split/**
+- tests/modules/nf-core/last/split/**
 
 last/train:
-  - modules/nf-core/last/train/**
-  - tests/modules/nf-core/last/train/**
+- modules/nf-core/last/train/**
+- tests/modules/nf-core/last/train/**
 
 leehom:
-  - modules/nf-core/leehom/**
-  - tests/modules/nf-core/leehom/**
+- modules/nf-core/leehom/**
+- tests/modules/nf-core/leehom/**
 
 legsta:
-  - modules/nf-core/legsta/**
-  - tests/modules/nf-core/legsta/**
+- modules/nf-core/legsta/**
+- tests/modules/nf-core/legsta/**
 
 lima:
-  - modules/nf-core/lima/**
-  - tests/modules/nf-core/lima/**
+- modules/nf-core/lima/**
+- tests/modules/nf-core/lima/**
 
 lissero:
-  - modules/nf-core/lissero/**
-  - tests/modules/nf-core/lissero/**
+- modules/nf-core/lissero/**
+- tests/modules/nf-core/lissero/**
 
 lofreq/call:
-  - modules/nf-core/lofreq/call/**
-  - tests/modules/nf-core/lofreq/call/**
+- modules/nf-core/lofreq/call/**
+- tests/modules/nf-core/lofreq/call/**
 
 lofreq/callparallel:
-  - modules/nf-core/lofreq/callparallel/**
-  - tests/modules/nf-core/lofreq/callparallel/**
+- modules/nf-core/lofreq/callparallel/**
+- tests/modules/nf-core/lofreq/callparallel/**
 
 lofreq/filter:
-  - modules/nf-core/lofreq/filter/**
-  - tests/modules/nf-core/lofreq/filter/**
+- modules/nf-core/lofreq/filter/**
+- tests/modules/nf-core/lofreq/filter/**
 
 lofreq/indelqual:
-  - modules/nf-core/lofreq/indelqual/**
-  - tests/modules/nf-core/lofreq/indelqual/**
+- modules/nf-core/lofreq/indelqual/**
+- tests/modules/nf-core/lofreq/indelqual/**
 
 macrel/contigs:
-  - modules/nf-core/macrel/contigs/**
-  - tests/modules/nf-core/macrel/contigs/**
+- modules/nf-core/macrel/contigs/**
+- tests/modules/nf-core/macrel/contigs/**
 
 macs2/callpeak:
-  - modules/nf-core/macs2/callpeak/**
-  - tests/modules/nf-core/macs2/callpeak/**
+- modules/nf-core/macs2/callpeak/**
+- tests/modules/nf-core/macs2/callpeak/**
 
 mafft:
-  - modules/nf-core/mafft/**
-  - tests/modules/nf-core/mafft/**
+- modules/nf-core/mafft/**
+- tests/modules/nf-core/mafft/**
 
 mageck/count:
-  - modules/nf-core/mageck/count/**
-  - tests/modules/nf-core/mageck/count/**
+- modules/nf-core/mageck/count/**
+- tests/modules/nf-core/mageck/count/**
 
 mageck/mle:
-  - modules/nf-core/mageck/mle/**
-  - tests/modules/nf-core/mageck/mle/**
+- modules/nf-core/mageck/mle/**
+- tests/modules/nf-core/mageck/mle/**
 
 malt/build:
-  - modules/nf-core/malt/build/**
-  - tests/modules/nf-core/malt/build_test/**
+- modules/nf-core/malt/build/**
+- tests/modules/nf-core/malt/build_test/**
 
 malt/run:
-  - modules/nf-core/malt/run/**
-  - tests/modules/nf-core/malt/run/**
+- modules/nf-core/malt/run/**
+- tests/modules/nf-core/malt/run/**
 
 maltextract:
-  - modules/nf-core/maltextract/**
-  - tests/modules/nf-core/maltextract/**
+- modules/nf-core/maltextract/**
+- tests/modules/nf-core/maltextract/**
 
 manta/convertinversion:
-  - modules/nf-core/manta/convertinversion/**
-  - tests/modules/nf-core/manta/convertinversion/**
+- modules/nf-core/manta/convertinversion/**
+- tests/modules/nf-core/manta/convertinversion/**
 
 manta/germline:
-  - modules/nf-core/manta/germline/**
-  - tests/modules/nf-core/manta/germline/**
+- modules/nf-core/manta/germline/**
+- tests/modules/nf-core/manta/germline/**
 
 manta/somatic:
-  - modules/nf-core/manta/somatic/**
-  - tests/modules/nf-core/manta/somatic/**
+- modules/nf-core/manta/somatic/**
+- tests/modules/nf-core/manta/somatic/**
 
 manta/tumoronly:
-  - modules/nf-core/manta/tumoronly/**
-  - tests/modules/nf-core/manta/tumoronly/**
+- modules/nf-core/manta/tumoronly/**
+- tests/modules/nf-core/manta/tumoronly/**
 
 mapdamage2:
-  - modules/nf-core/mapdamage2/**
-  - tests/modules/nf-core/mapdamage2/**
+- modules/nf-core/mapdamage2/**
+- tests/modules/nf-core/mapdamage2/**
 
 mash/dist:
-  - modules/nf-core/mash/dist/**
-  - tests/modules/nf-core/mash/dist/**
+- modules/nf-core/mash/dist/**
+- tests/modules/nf-core/mash/dist/**
 
 mash/screen:
-  - modules/nf-core/mash/screen/**
-  - tests/modules/nf-core/mash/screen/**
+- modules/nf-core/mash/screen/**
+- tests/modules/nf-core/mash/screen/**
 
 mash/sketch:
-  - modules/nf-core/mash/sketch/**
-  - tests/modules/nf-core/mash/sketch/**
+- modules/nf-core/mash/sketch/**
+- tests/modules/nf-core/mash/sketch/**
 
 mashtree:
-  - modules/nf-core/mashtree/**
-  - tests/modules/nf-core/mashtree/**
+- modules/nf-core/mashtree/**
+- tests/modules/nf-core/mashtree/**
 
 maxbin2:
-  - modules/nf-core/maxbin2/**
-  - tests/modules/nf-core/maxbin2/**
+- modules/nf-core/maxbin2/**
+- tests/modules/nf-core/maxbin2/**
 
 maxquant/lfq:
-  - modules/nf-core/maxquant/lfq/**
-  - tests/modules/nf-core/maxquant/lfq/**
+- modules/nf-core/maxquant/lfq/**
+- tests/modules/nf-core/maxquant/lfq/**
 
 mcroni:
-  - modules/nf-core/mcroni/**
-  - tests/modules/nf-core/mcroni/**
+- modules/nf-core/mcroni/**
+- tests/modules/nf-core/mcroni/**
 
 md5sum:
-  - modules/nf-core/md5sum/**
-  - tests/modules/nf-core/md5sum/**
+- modules/nf-core/md5sum/**
+- tests/modules/nf-core/md5sum/**
 
 medaka:
-  - modules/nf-core/medaka/**
-  - tests/modules/nf-core/medaka/**
+- modules/nf-core/medaka/**
+- tests/modules/nf-core/medaka/**
 
 megahit:
-  - modules/nf-core/megahit/**
-  - tests/modules/nf-core/megahit/**
+- modules/nf-core/megahit/**
+- tests/modules/nf-core/megahit/**
 
 megan/daa2info:
-  - modules/nf-core/megan/daa2info/**
-  - tests/modules/nf-core/megan/daa2info/**
+- modules/nf-core/megan/daa2info/**
+- tests/modules/nf-core/megan/daa2info/**
 
 megan/rma2info:
-  - modules/nf-core/megan/rma2info/**
-  - tests/modules/nf-core/megan/rma2info/**
+- modules/nf-core/megan/rma2info/**
+- tests/modules/nf-core/megan/rma2info/**
 
 meningotype:
-  - modules/nf-core/meningotype/**
-  - tests/modules/nf-core/meningotype/**
+- modules/nf-core/meningotype/**
+- tests/modules/nf-core/meningotype/**
 
 merqury:
-  - modules/nf-core/merqury/**
-  - tests/modules/nf-core/merqury/**
+- modules/nf-core/merqury/**
+- tests/modules/nf-core/merqury/**
 
 merquryfk/katcomp:
-  - modules/nf-core/merquryfk/katcomp/**
-  - tests/modules/nf-core/merquryfk/katcomp/**
+- modules/nf-core/merquryfk/katcomp/**
+- tests/modules/nf-core/merquryfk/katcomp/**
 
 merquryfk/katgc:
-  - modules/nf-core/merquryfk/katgc/**
-  - tests/modules/nf-core/merquryfk/katgc/**
+- modules/nf-core/merquryfk/katgc/**
+- tests/modules/nf-core/merquryfk/katgc/**
 
 merquryfk/merquryfk:
-  - modules/nf-core/merquryfk/merquryfk/**
-  - tests/modules/nf-core/merquryfk/merquryfk/**
+- modules/nf-core/merquryfk/merquryfk/**
+- tests/modules/nf-core/merquryfk/merquryfk/**
 
 merquryfk/ploidyplot:
-  - modules/nf-core/merquryfk/ploidyplot/**
-  - tests/modules/nf-core/merquryfk/ploidyplot/**
+- modules/nf-core/merquryfk/ploidyplot/**
+- tests/modules/nf-core/merquryfk/ploidyplot/**
 
 meryl/count:
-  - modules/nf-core/meryl/count/**
-  - tests/modules/nf-core/meryl/count/**
+- modules/nf-core/meryl/count/**
+- tests/modules/nf-core/meryl/count/**
 
 meryl/histogram:
-  - modules/nf-core/meryl/histogram/**
-  - tests/modules/nf-core/meryl/histogram/**
+- modules/nf-core/meryl/histogram/**
+- tests/modules/nf-core/meryl/histogram/**
 
 meryl/unionsum:
-  - modules/nf-core/meryl/unionsum/**
-  - tests/modules/nf-core/meryl/unionsum/**
+- modules/nf-core/meryl/unionsum/**
+- tests/modules/nf-core/meryl/unionsum/**
 
 metabat2/jgisummarizebamcontigdepths:
-  - modules/nf-core/metabat2/jgisummarizebamcontigdepths/**
-  - tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/**
+- modules/nf-core/metabat2/jgisummarizebamcontigdepths/**
+- tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/**
 
 metabat2/metabat2:
-  - modules/nf-core/metabat2/metabat2/**
-  - tests/modules/nf-core/metabat2/metabat2/**
+- modules/nf-core/metabat2/metabat2/**
+- tests/modules/nf-core/metabat2/metabat2/**
 
 metaphlan3/mergemetaphlantables:
-  - modules/nf-core/metaphlan3/mergemetaphlantables/**
-  - tests/modules/nf-core/metaphlan3/mergemetaphlantables/**
+- modules/nf-core/metaphlan3/mergemetaphlantables/**
+- tests/modules/nf-core/metaphlan3/mergemetaphlantables/**
 
 metaphlan3/metaphlan3:
-  - modules/nf-core/metaphlan3/metaphlan3/**
-  - tests/modules/nf-core/metaphlan3/metaphlan3/**
+- modules/nf-core/metaphlan3/metaphlan3/**
+- tests/modules/nf-core/metaphlan3/metaphlan3/**
 
 methyldackel/extract:
-  - modules/nf-core/methyldackel/extract/**
-  - tests/modules/nf-core/methyldackel/extract/**
+- modules/nf-core/methyldackel/extract/**
+- tests/modules/nf-core/methyldackel/extract/**
 
 methyldackel/mbias:
-  - modules/nf-core/methyldackel/mbias/**
-  - tests/modules/nf-core/methyldackel/mbias/**
+- modules/nf-core/methyldackel/mbias/**
+- tests/modules/nf-core/methyldackel/mbias/**
 
 minia:
-  - modules/nf-core/minia/**
-  - tests/modules/nf-core/minia/**
+- modules/nf-core/minia/**
+- tests/modules/nf-core/minia/**
 
 miniasm:
-  - modules/nf-core/miniasm/**
-  - tests/modules/nf-core/miniasm/**
+- modules/nf-core/miniasm/**
+- tests/modules/nf-core/miniasm/**
 
 minimap2/align:
-  - modules/nf-core/minimap2/align/**
-  - tests/modules/nf-core/minimap2/align/**
+- modules/nf-core/minimap2/align/**
+- tests/modules/nf-core/minimap2/align/**
 
 minimap2/index:
-  - modules/nf-core/minimap2/index/**
-  - tests/modules/nf-core/minimap2/index/**
+- modules/nf-core/minimap2/index/**
+- tests/modules/nf-core/minimap2/index/**
 
 miranda:
-  - modules/nf-core/miranda/**
-  - tests/modules/nf-core/miranda/**
+- modules/nf-core/miranda/**
+- tests/modules/nf-core/miranda/**
 
 mlst:
-  - modules/nf-core/mlst/**
-  - tests/modules/nf-core/mlst/**
+- modules/nf-core/mlst/**
+- tests/modules/nf-core/mlst/**
 
 mobsuite/recon:
-  - modules/nf-core/mobsuite/recon/**
-  - tests/modules/nf-core/mobsuite/recon/**
+- modules/nf-core/mobsuite/recon/**
+- tests/modules/nf-core/mobsuite/recon/**
 
 mosdepth:
-  - modules/nf-core/mosdepth/**
-  - tests/modules/nf-core/mosdepth/**
+- modules/nf-core/mosdepth/**
+- tests/modules/nf-core/mosdepth/**
 
 motus/downloaddb:
-  - modules/nf-core/motus/downloaddb/**
-  - tests/modules/nf-core/motus/downloaddb/**
+- modules/nf-core/motus/downloaddb/**
+- tests/modules/nf-core/motus/downloaddb/**
 
 motus/merge:
-  - modules/nf-core/motus/merge/**
-  - tests/modules/nf-core/motus/merge/**
+- modules/nf-core/motus/merge/**
+- tests/modules/nf-core/motus/merge/**
 
 motus/profile:
-  - modules/nf-core/motus/profile/**
-  - tests/modules/nf-core/motus/profile/**
+- modules/nf-core/motus/profile/**
+- tests/modules/nf-core/motus/profile/**
 
 msisensor/msi:
-  - modules/nf-core/msisensor/msi/**
-  - tests/modules/nf-core/msisensor/msi/**
+- modules/nf-core/msisensor/msi/**
+- tests/modules/nf-core/msisensor/msi/**
 
 msisensor/scan:
-  - modules/nf-core/msisensor/scan/**
-  - tests/modules/nf-core/msisensor/scan/**
+- modules/nf-core/msisensor/scan/**
+- tests/modules/nf-core/msisensor/scan/**
 
 msisensor2/msi:
-  - modules/nf-core/msisensor2/msi/**
-  - tests/modules/nf-core/msisensor2/msi/**
+- modules/nf-core/msisensor2/msi/**
+- tests/modules/nf-core/msisensor2/msi/**
 
 msisensor2/scan:
-  - modules/nf-core/msisensor2/scan/**
-  - tests/modules/nf-core/msisensor2/scan/**
+- modules/nf-core/msisensor2/scan/**
+- tests/modules/nf-core/msisensor2/scan/**
 
 msisensorpro/msi_somatic:
-  - modules/nf-core/msisensorpro/msi_somatic/**
-  - tests/modules/nf-core/msisensorpro/msi_somatic/**
+- modules/nf-core/msisensorpro/msi_somatic/**
+- tests/modules/nf-core/msisensorpro/msi_somatic/**
 
 msisensorpro/scan:
-  - modules/nf-core/msisensorpro/scan/**
-  - tests/modules/nf-core/msisensorpro/scan/**
+- modules/nf-core/msisensorpro/scan/**
+- tests/modules/nf-core/msisensorpro/scan/**
 
 mtnucratio:
-  - modules/nf-core/mtnucratio/**
-  - tests/modules/nf-core/mtnucratio/**
+- modules/nf-core/mtnucratio/**
+- tests/modules/nf-core/mtnucratio/**
 
 multiqc:
-  - modules/nf-core/fastqc/**
-  - modules/nf-core/multiqc/**
-  - tests/modules/nf-core/multiqc/**
+- modules/nf-core/fastqc/**
+- modules/nf-core/multiqc/**
+- tests/modules/nf-core/multiqc/**
 
 multivcfanalyzer:
-  - modules/nf-core/multivcfanalyzer/**
-  - tests/modules/nf-core/multivcfanalyzer/**
+- modules/nf-core/multivcfanalyzer/**
+- tests/modules/nf-core/multivcfanalyzer/**
 
 mummer:
-  - modules/nf-core/mummer/**
-  - tests/modules/nf-core/mummer/**
+- modules/nf-core/mummer/**
+- tests/modules/nf-core/mummer/**
 
 muscle:
-  - modules/nf-core/muscle/**
-  - tests/modules/nf-core/muscle/**
+- modules/nf-core/muscle/**
+- tests/modules/nf-core/muscle/**
 
 mykrobe/predict:
-  - modules/nf-core/mykrobe/predict/**
-  - tests/modules/nf-core/mykrobe/predict/**
+- modules/nf-core/mykrobe/predict/**
+- tests/modules/nf-core/mykrobe/predict/**
 
 nanolyse:
-  - modules/nf-core/nanolyse/**
-  - tests/modules/nf-core/nanolyse/**
+- modules/nf-core/nanolyse/**
+- tests/modules/nf-core/nanolyse/**
 
 nanomonsv/parse:
-  - modules/nf-core/nanomonsv/parse/**
-  - tests/modules/nf-core/nanomonsv/parse/**
+- modules/nf-core/nanomonsv/parse/**
+- tests/modules/nf-core/nanomonsv/parse/**
 
 nanoplot:
-  - modules/nf-core/nanoplot/**
-  - tests/modules/nf-core/nanoplot/**
+- modules/nf-core/nanoplot/**
+- tests/modules/nf-core/nanoplot/**
 
 ncbigenomedownload:
-  - modules/nf-core/ncbigenomedownload/**
-  - tests/modules/nf-core/ncbigenomedownload/**
+- modules/nf-core/ncbigenomedownload/**
+- tests/modules/nf-core/ncbigenomedownload/**
 
 nextclade/datasetget:
-  - modules/nf-core/nextclade/datasetget/**
-  - tests/modules/nf-core/nextclade/datasetget/**
+- modules/nf-core/nextclade/datasetget/**
+- tests/modules/nf-core/nextclade/datasetget/**
 
 nextclade/run:
-  - modules/nf-core/nextclade/run/**
-  - tests/modules/nf-core/nextclade/run/**
+- modules/nf-core/nextclade/run/**
+- tests/modules/nf-core/nextclade/run/**
 
 nextgenmap:
-  - modules/nf-core/nextgenmap/**
-  - tests/modules/nf-core/nextgenmap/**
+- modules/nf-core/nextgenmap/**
+- tests/modules/nf-core/nextgenmap/**
 
 ngmaster:
-  - modules/nf-core/ngmaster/**
-  - tests/modules/nf-core/ngmaster/**
+- modules/nf-core/ngmaster/**
+- tests/modules/nf-core/ngmaster/**
 
 ngscheckmate/ncm:
-  - modules/nf-core/ngscheckmate/ncm/**
-  - tests/modules/nf-core/ngscheckmate/ncm/**
+- modules/nf-core/ngscheckmate/ncm/**
+- tests/modules/nf-core/ngscheckmate/ncm/**
 
 nucmer:
-  - modules/nf-core/nucmer/**
-  - tests/modules/nf-core/nucmer/**
+- modules/nf-core/nucmer/**
+- tests/modules/nf-core/nucmer/**
 
 odgi/build:
-  - modules/nf-core/odgi/build/**
-  - tests/modules/nf-core/odgi/build_test/**
+- modules/nf-core/odgi/build/**
+- tests/modules/nf-core/odgi/build_test/**
 
 odgi/draw:
-  - modules/nf-core/odgi/draw/**
-  - tests/modules/nf-core/odgi/draw/**
+- modules/nf-core/odgi/draw/**
+- tests/modules/nf-core/odgi/draw/**
 
 odgi/layout:
-  - modules/nf-core/odgi/layout/**
-  - tests/modules/nf-core/odgi/layout/**
+- modules/nf-core/odgi/layout/**
+- tests/modules/nf-core/odgi/layout/**
 
 odgi/sort:
-  - modules/nf-core/odgi/sort/**
-  - tests/modules/nf-core/odgi/sort/**
+- modules/nf-core/odgi/sort/**
+- tests/modules/nf-core/odgi/sort/**
 
 odgi/stats:
-  - modules/nf-core/odgi/stats/**
-  - tests/modules/nf-core/odgi/stats/**
+- modules/nf-core/odgi/stats/**
+- tests/modules/nf-core/odgi/stats/**
 
 odgi/unchop:
-  - modules/nf-core/odgi/unchop/**
-  - tests/modules/nf-core/odgi/unchop/**
+- modules/nf-core/odgi/unchop/**
+- tests/modules/nf-core/odgi/unchop/**
 
 odgi/view:
-  - modules/nf-core/odgi/view/**
-  - tests/modules/nf-core/odgi/view/**
+- modules/nf-core/odgi/view/**
+- tests/modules/nf-core/odgi/view/**
 
 odgi/viz:
-  - modules/nf-core/odgi/viz/**
-  - tests/modules/nf-core/odgi/viz/**
+- modules/nf-core/odgi/viz/**
+- tests/modules/nf-core/odgi/viz/**
 
 optitype:
-  - modules/nf-core/optitype/**
-  - tests/modules/nf-core/optitype/**
+- modules/nf-core/optitype/**
+- tests/modules/nf-core/optitype/**
 
 pairix:
-  - modules/nf-core/pairix/**
-  - tests/modules/nf-core/pairix/**
+- modules/nf-core/pairix/**
+- tests/modules/nf-core/pairix/**
 
 pairtools/dedup:
-  - modules/nf-core/pairtools/dedup/**
-  - tests/modules/nf-core/pairtools/dedup/**
+- modules/nf-core/pairtools/dedup/**
+- tests/modules/nf-core/pairtools/dedup/**
 
 pairtools/flip:
-  - modules/nf-core/pairtools/flip/**
-  - tests/modules/nf-core/pairtools/flip/**
+- modules/nf-core/pairtools/flip/**
+- tests/modules/nf-core/pairtools/flip/**
 
 pairtools/parse:
-  - modules/nf-core/pairtools/parse/**
-  - tests/modules/nf-core/pairtools/parse/**
+- modules/nf-core/pairtools/parse/**
+- tests/modules/nf-core/pairtools/parse/**
 
 pairtools/restrict:
-  - modules/nf-core/pairtools/restrict/**
-  - tests/modules/nf-core/pairtools/restrict/**
+- modules/nf-core/pairtools/restrict/**
+- tests/modules/nf-core/pairtools/restrict/**
 
 pairtools/select:
-  - modules/nf-core/pairtools/select/**
-  - tests/modules/nf-core/pairtools/select/**
+- modules/nf-core/pairtools/select/**
+- tests/modules/nf-core/pairtools/select/**
 
 pairtools/sort:
-  - modules/nf-core/pairtools/sort/**
-  - tests/modules/nf-core/pairtools/sort/**
+- modules/nf-core/pairtools/sort/**
+- tests/modules/nf-core/pairtools/sort/**
 
 panaroo/run:
-  - modules/nf-core/panaroo/run/**
-  - tests/modules/nf-core/panaroo/run/**
+- modules/nf-core/panaroo/run/**
+- tests/modules/nf-core/panaroo/run/**
 
 pangolin:
-  - modules/nf-core/pangolin/**
-  - tests/modules/nf-core/pangolin/**
+- modules/nf-core/pangolin/**
+- tests/modules/nf-core/pangolin/**
 
 paraclu:
-  - modules/nf-core/paraclu/**
-  - tests/modules/nf-core/paraclu/**
+- modules/nf-core/paraclu/**
+- tests/modules/nf-core/paraclu/**
 
 pasty:
-  - modules/nf-core/pasty/**
-  - tests/modules/nf-core/pasty/**
+- modules/nf-core/pasty/**
+- tests/modules/nf-core/pasty/**
 
 pbbam/pbmerge:
-  - modules/nf-core/pbbam/pbmerge/**
-  - tests/modules/nf-core/pbbam/pbmerge/**
+- modules/nf-core/pbbam/pbmerge/**
+- tests/modules/nf-core/pbbam/pbmerge/**
 
 pbccs:
-  - modules/nf-core/pbccs/**
-  - tests/modules/nf-core/pbccs/**
+- modules/nf-core/pbccs/**
+- tests/modules/nf-core/pbccs/**
 
 pbptyper:
-  - modules/nf-core/pbptyper/**
-  - tests/modules/nf-core/pbptyper/**
+- modules/nf-core/pbptyper/**
+- tests/modules/nf-core/pbptyper/**
 
 pear:
-  - modules/nf-core/pear/**
-  - tests/modules/nf-core/pear/**
+- modules/nf-core/pear/**
+- tests/modules/nf-core/pear/**
 
 peddy:
-  - modules/nf-core/peddy/**
-  - tests/modules/nf-core/peddy/**
+- modules/nf-core/peddy/**
+- tests/modules/nf-core/peddy/**
 
 phantompeakqualtools:
-  - modules/nf-core/phantompeakqualtools/**
-  - tests/modules/nf-core/phantompeakqualtools/**
+- modules/nf-core/phantompeakqualtools/**
+- tests/modules/nf-core/phantompeakqualtools/**
 
 phyloflash:
-  - modules/nf-core/phyloflash/**
-  - tests/modules/nf-core/phyloflash/**
+- modules/nf-core/phyloflash/**
+- tests/modules/nf-core/phyloflash/**
 
 picard/addorreplacereadgroups:
-  - modules/nf-core/picard/addorreplacereadgroups/**
-  - tests/modules/nf-core/picard/addorreplacereadgroups/**
+- modules/nf-core/picard/addorreplacereadgroups/**
+- tests/modules/nf-core/picard/addorreplacereadgroups/**
 
 picard/cleansam:
-  - modules/nf-core/picard/cleansam/**
-  - tests/modules/nf-core/picard/cleansam/**
+- modules/nf-core/picard/cleansam/**
+- tests/modules/nf-core/picard/cleansam/**
 
 picard/collecthsmetrics:
-  - modules/nf-core/picard/collecthsmetrics/**
-  - tests/modules/nf-core/picard/collecthsmetrics/**
+- modules/nf-core/picard/collecthsmetrics/**
+- tests/modules/nf-core/picard/collecthsmetrics/**
 
 picard/collectmultiplemetrics:
-  - modules/nf-core/picard/collectmultiplemetrics/**
-  - tests/modules/nf-core/picard/collectmultiplemetrics/**
+- modules/nf-core/picard/collectmultiplemetrics/**
+- tests/modules/nf-core/picard/collectmultiplemetrics/**
 
 picard/collectwgsmetrics:
-  - modules/nf-core/picard/collectwgsmetrics/**
-  - tests/modules/nf-core/picard/collectwgsmetrics/**
+- modules/nf-core/picard/collectwgsmetrics/**
+- tests/modules/nf-core/picard/collectwgsmetrics/**
 
 picard/createsequencedictionary:
-  - modules/nf-core/picard/createsequencedictionary/**
-  - tests/modules/nf-core/picard/createsequencedictionary/**
+- modules/nf-core/picard/createsequencedictionary/**
+- tests/modules/nf-core/picard/createsequencedictionary/**
 
 picard/crosscheckfingerprints:
-  - modules/nf-core/picard/crosscheckfingerprints/**
-  - tests/modules/nf-core/picard/crosscheckfingerprints/**
+- modules/nf-core/picard/crosscheckfingerprints/**
+- tests/modules/nf-core/picard/crosscheckfingerprints/**
 
 picard/fastqtosam:
-  - modules/nf-core/picard/fastqtosam/**
-  - tests/modules/nf-core/picard/fastqtosam/**
+- modules/nf-core/picard/fastqtosam/**
+- tests/modules/nf-core/picard/fastqtosam/**
 
 picard/filtersamreads:
-  - modules/nf-core/picard/filtersamreads/**
-  - tests/modules/nf-core/picard/filtersamreads/**
+- modules/nf-core/picard/filtersamreads/**
+- tests/modules/nf-core/picard/filtersamreads/**
 
 picard/fixmateinformation:
-  - modules/nf-core/picard/fixmateinformation/**
-  - tests/modules/nf-core/picard/fixmateinformation/**
+- modules/nf-core/picard/fixmateinformation/**
+- tests/modules/nf-core/picard/fixmateinformation/**
 
 picard/liftovervcf:
-  - modules/nf-core/picard/liftovervcf/**
-  - tests/modules/nf-core/picard/liftovervcf/**
+- modules/nf-core/picard/liftovervcf/**
+- tests/modules/nf-core/picard/liftovervcf/**
 
 picard/markduplicates:
-  - modules/nf-core/picard/markduplicates/**
-  - tests/modules/nf-core/picard/markduplicates/**
+- modules/nf-core/picard/markduplicates/**
+- tests/modules/nf-core/picard/markduplicates/**
 
 picard/mergesamfiles:
-  - modules/nf-core/picard/mergesamfiles/**
-  - tests/modules/nf-core/picard/mergesamfiles/**
+- modules/nf-core/picard/mergesamfiles/**
+- tests/modules/nf-core/picard/mergesamfiles/**
 
 picard/renamesampleinvcf:
-  - modules/nf-core/picard/renamesampleinvcf/**
-  - tests/modules/nf-core/picard/renamesampleinvcf/**
+- modules/nf-core/picard/renamesampleinvcf/**
+- tests/modules/nf-core/picard/renamesampleinvcf/**
 
 picard/sortsam:
-  - modules/nf-core/picard/sortsam/**
-  - tests/modules/nf-core/picard/sortsam/**
+- modules/nf-core/picard/sortsam/**
+- tests/modules/nf-core/picard/sortsam/**
 
 picard/sortvcf:
-  - modules/nf-core/picard/sortvcf/**
-  - tests/modules/nf-core/picard/sortvcf/**
+- modules/nf-core/picard/sortvcf/**
+- tests/modules/nf-core/picard/sortvcf/**
 
 pints/caller:
-  - modules/nf-core/pints/caller/**
-  - tests/modules/nf-core/pints/caller/**
+- modules/nf-core/pints/caller/**
+- tests/modules/nf-core/pints/caller/**
 
 pirate:
-  - modules/nf-core/pirate/**
-  - tests/modules/nf-core/pirate/**
+- modules/nf-core/pirate/**
+- tests/modules/nf-core/pirate/**
 
 plasmidfinder:
-  - modules/nf-core/plasmidfinder/**
-  - tests/modules/nf-core/plasmidfinder/**
+- modules/nf-core/plasmidfinder/**
+- tests/modules/nf-core/plasmidfinder/**
 
 plasmidid:
-  - modules/nf-core/plasmidid/**
-  - tests/modules/nf-core/plasmidid/**
+- modules/nf-core/plasmidid/**
+- tests/modules/nf-core/plasmidid/**
 
 plink/extract:
-  - modules/nf-core/plink/extract/**
-  - tests/modules/nf-core/plink/extract/**
+- modules/nf-core/plink/extract/**
+- tests/modules/nf-core/plink/extract/**
 
 plink/vcf:
-  - modules/nf-core/plink/vcf/**
-  - tests/modules/nf-core/plink/vcf/**
+- modules/nf-core/plink/vcf/**
+- tests/modules/nf-core/plink/vcf/**
 
 plink2/extract:
-  - modules/nf-core/plink2/extract/**
-  - tests/modules/nf-core/plink2/extract/**
+- modules/nf-core/plink2/extract/**
+- tests/modules/nf-core/plink2/extract/**
 
 plink2/score:
-  - modules/nf-core/plink2/score/**
-  - tests/modules/nf-core/plink2/score/**
+- modules/nf-core/plink2/score/**
+- tests/modules/nf-core/plink2/score/**
 
 plink2/vcf:
-  - modules/nf-core/plink2/vcf/**
-  - tests/modules/nf-core/plink2/vcf/**
+- modules/nf-core/plink2/vcf/**
+- tests/modules/nf-core/plink2/vcf/**
 
 pmdtools/filter:
-  - modules/nf-core/pmdtools/filter/**
-  - tests/modules/nf-core/pmdtools/filter/**
+- modules/nf-core/pmdtools/filter/**
+- tests/modules/nf-core/pmdtools/filter/**
 
 porechop:
-  - modules/nf-core/porechop/**
-  - tests/modules/nf-core/porechop/**
+- modules/nf-core/porechop/**
+- tests/modules/nf-core/porechop/**
 
 preseq/ccurve:
-  - modules/nf-core/preseq/ccurve/**
-  - tests/modules/nf-core/preseq/ccurve/**
+- modules/nf-core/preseq/ccurve/**
+- tests/modules/nf-core/preseq/ccurve/**
 
 preseq/lcextrap:
-  - modules/nf-core/preseq/lcextrap/**
-  - tests/modules/nf-core/preseq/lcextrap/**
+- modules/nf-core/preseq/lcextrap/**
+- tests/modules/nf-core/preseq/lcextrap/**
 
 pretextmap:
-  - modules/nf-core/pretextmap/**
-  - tests/modules/nf-core/pretextmap/**
+- modules/nf-core/pretextmap/**
+- tests/modules/nf-core/pretextmap/**
 
 prinseqplusplus:
-  - modules/nf-core/prinseqplusplus/**
-  - tests/modules/nf-core/prinseqplusplus/**
+- modules/nf-core/prinseqplusplus/**
+- tests/modules/nf-core/prinseqplusplus/**
 
 prodigal:
-  - modules/nf-core/prodigal/**
-  - tests/modules/nf-core/prodigal/**
+- modules/nf-core/prodigal/**
+- tests/modules/nf-core/prodigal/**
 
 prokka:
-  - modules/nf-core/prokka/**
-  - tests/modules/nf-core/prokka/**
+- modules/nf-core/prokka/**
+- tests/modules/nf-core/prokka/**
 
 pycoqc:
-  - modules/nf-core/pycoqc/**
-  - tests/modules/nf-core/pycoqc/**
+- modules/nf-core/pycoqc/**
+- tests/modules/nf-core/pycoqc/**
 
 pydamage/analyze:
-  - modules/nf-core/pydamage/analyze/**
-  - tests/modules/nf-core/pydamage/analyze/**
+- modules/nf-core/pydamage/analyze/**
+- tests/modules/nf-core/pydamage/analyze/**
 
 pydamage/filter:
-  - modules/nf-core/pydamage/filter/**
-  - tests/modules/nf-core/pydamage/filter/**
+- modules/nf-core/pydamage/filter/**
+- tests/modules/nf-core/pydamage/filter/**
 
 qcat:
-  - modules/nf-core/qcat/**
-  - tests/modules/nf-core/qcat/**
+- modules/nf-core/qcat/**
+- tests/modules/nf-core/qcat/**
 
 qualimap/bamqc:
-  - modules/nf-core/qualimap/bamqc/**
-  - tests/modules/nf-core/qualimap/bamqc/**
+- modules/nf-core/qualimap/bamqc/**
+- tests/modules/nf-core/qualimap/bamqc/**
 
 qualimap/bamqccram:
-  - modules/nf-core/qualimap/bamqccram/**
-  - tests/modules/nf-core/qualimap/bamqccram/**
+- modules/nf-core/qualimap/bamqccram/**
+- tests/modules/nf-core/qualimap/bamqccram/**
 
 quast:
-  - modules/nf-core/quast/**
-  - tests/modules/nf-core/quast/**
+- modules/nf-core/quast/**
+- tests/modules/nf-core/quast/**
 
 racon:
-  - modules/nf-core/racon/**
-  - tests/modules/nf-core/racon/**
+- modules/nf-core/racon/**
+- tests/modules/nf-core/racon/**
 
 rapidnj:
-  - modules/nf-core/rapidnj/**
-  - tests/modules/nf-core/rapidnj/**
+- modules/nf-core/rapidnj/**
+- tests/modules/nf-core/rapidnj/**
 
 rasusa:
-  - modules/nf-core/rasusa/**
-  - tests/modules/nf-core/rasusa/**
+- modules/nf-core/rasusa/**
+- tests/modules/nf-core/rasusa/**
 
 raven:
-  - modules/nf-core/raven/**
-  - tests/modules/nf-core/raven/**
+- modules/nf-core/raven/**
+- tests/modules/nf-core/raven/**
 
 raxmlng:
-  - modules/nf-core/raxmlng/**
-  - tests/modules/nf-core/raxmlng/**
+- modules/nf-core/raxmlng/**
+- tests/modules/nf-core/raxmlng/**
 
 rgi/main:
-  - modules/nf-core/rgi/main/**
-  - tests/modules/nf-core/rgi/main/**
+- modules/nf-core/rgi/main/**
+- tests/modules/nf-core/rgi/main/**
 
 rhocall/annotate:
-  - modules/nf-core/rhocall/annotate/**
-  - tests/modules/nf-core/rhocall/annotate/**
+- modules/nf-core/rhocall/annotate/**
+- tests/modules/nf-core/rhocall/annotate/**
 
 rmarkdownnotebook:
-  - modules/nf-core/rmarkdownnotebook/**
-  - tests/modules/nf-core/rmarkdownnotebook/**
+- modules/nf-core/rmarkdownnotebook/**
+- tests/modules/nf-core/rmarkdownnotebook/**
 
 roary:
-  - modules/nf-core/roary/**
-  - tests/modules/nf-core/roary/**
+- modules/nf-core/roary/**
+- tests/modules/nf-core/roary/**
 
 rsem/calculateexpression:
-  - modules/nf-core/rsem/calculateexpression/**
-  - tests/modules/nf-core/rsem/calculateexpression/**
+- modules/nf-core/rsem/calculateexpression/**
+- tests/modules/nf-core/rsem/calculateexpression/**
 
 rsem/preparereference:
-  - modules/nf-core/rsem/preparereference/**
-  - tests/modules/nf-core/rsem/preparereference/**
+- modules/nf-core/rsem/preparereference/**
+- tests/modules/nf-core/rsem/preparereference/**
 
 rseqc/bamstat:
-  - modules/nf-core/rseqc/bamstat/**
-  - tests/modules/nf-core/rseqc/bamstat/**
+- modules/nf-core/rseqc/bamstat/**
+- tests/modules/nf-core/rseqc/bamstat/**
 
 rseqc/inferexperiment:
-  - modules/nf-core/rseqc/inferexperiment/**
-  - tests/modules/nf-core/rseqc/inferexperiment/**
+- modules/nf-core/rseqc/inferexperiment/**
+- tests/modules/nf-core/rseqc/inferexperiment/**
 
 rseqc/innerdistance:
-  - modules/nf-core/rseqc/innerdistance/**
-  - tests/modules/nf-core/rseqc/innerdistance/**
+- modules/nf-core/rseqc/innerdistance/**
+- tests/modules/nf-core/rseqc/innerdistance/**
 
 rseqc/junctionannotation:
-  - modules/nf-core/rseqc/junctionannotation/**
-  - tests/modules/nf-core/rseqc/junctionannotation/**
+- modules/nf-core/rseqc/junctionannotation/**
+- tests/modules/nf-core/rseqc/junctionannotation/**
 
 rseqc/junctionsaturation:
-  - modules/nf-core/rseqc/junctionsaturation/**
-  - tests/modules/nf-core/rseqc/junctionsaturation/**
+- modules/nf-core/rseqc/junctionsaturation/**
+- tests/modules/nf-core/rseqc/junctionsaturation/**
 
 rseqc/readdistribution:
-  - modules/nf-core/rseqc/readdistribution/**
-  - tests/modules/nf-core/rseqc/readdistribution/**
+- modules/nf-core/rseqc/readdistribution/**
+- tests/modules/nf-core/rseqc/readdistribution/**
 
 rseqc/readduplication:
-  - modules/nf-core/rseqc/readduplication/**
-  - tests/modules/nf-core/rseqc/readduplication/**
+- modules/nf-core/rseqc/readduplication/**
+- tests/modules/nf-core/rseqc/readduplication/**
 
 rseqc/tin:
-  - modules/nf-core/rseqc/tin/**
-  - tests/modules/nf-core/rseqc/tin/**
+- modules/nf-core/rseqc/tin/**
+- tests/modules/nf-core/rseqc/tin/**
 
 rtgtools/pedfilter:
-  - modules/nf-core/rtgtools/pedfilter/**
-  - tests/modules/nf-core/rtgtools/pedfilter/**
+- modules/nf-core/rtgtools/pedfilter/**
+- tests/modules/nf-core/rtgtools/pedfilter/**
 
 rtgtools/vcfeval:
-  - modules/nf-core/rtgtools/vcfeval/**
-  - tests/modules/nf-core/rtgtools/vcfeval/**
+- modules/nf-core/rtgtools/vcfeval/**
+- tests/modules/nf-core/rtgtools/vcfeval/**
 
 salmon/index:
-  - modules/nf-core/salmon/index/**
-  - tests/modules/nf-core/salmon/index/**
+- modules/nf-core/salmon/index/**
+- tests/modules/nf-core/salmon/index/**
 
 salmon/quant:
-  - modules/nf-core/salmon/quant/**
-  - tests/modules/nf-core/salmon/quant/**
+- modules/nf-core/salmon/quant/**
+- tests/modules/nf-core/salmon/quant/**
 
 samblaster:
-  - modules/nf-core/samblaster/**
-  - tests/modules/nf-core/samblaster/**
+- modules/nf-core/samblaster/**
+- tests/modules/nf-core/samblaster/**
 
 samtools/ampliconclip:
-  - modules/nf-core/samtools/ampliconclip/**
-  - tests/modules/nf-core/samtools/ampliconclip/**
+- modules/nf-core/samtools/ampliconclip/**
+- tests/modules/nf-core/samtools/ampliconclip/**
 
 samtools/bam2fq:
-  - modules/nf-core/samtools/bam2fq/**
-  - tests/modules/nf-core/samtools/bam2fq/**
+- modules/nf-core/samtools/bam2fq/**
+- tests/modules/nf-core/samtools/bam2fq/**
 
 samtools/calmd:
-  - modules/nf-core/samtools/calmd/**
-  - tests/modules/nf-core/samtools/calmd/**
+- modules/nf-core/samtools/calmd/**
+- tests/modules/nf-core/samtools/calmd/**
 
 samtools/collate:
-  - modules/nf-core/samtools/collate/**
-  - tests/modules/nf-core/samtools/collate/**
+- modules/nf-core/samtools/collate/**
+- tests/modules/nf-core/samtools/collate/**
 
 samtools/collatefastq:
-  - modules/nf-core/samtools/collatefastq/**
-  - tests/modules/nf-core/samtools/collatefastq/**
+- modules/nf-core/samtools/collatefastq/**
+- tests/modules/nf-core/samtools/collatefastq/**
 
 samtools/convert:
-  - modules/nf-core/samtools/convert/**
-  - tests/modules/nf-core/samtools/convert/**
+- modules/nf-core/samtools/convert/**
+- tests/modules/nf-core/samtools/convert/**
 
 samtools/depth:
-  - modules/nf-core/samtools/depth/**
-  - tests/modules/nf-core/samtools/depth/**
+- modules/nf-core/samtools/depth/**
+- tests/modules/nf-core/samtools/depth/**
 
 samtools/dict:
-  - modules/nf-core/samtools/dict/**
-  - tests/modules/nf-core/samtools/dict/**
+- modules/nf-core/samtools/dict/**
+- tests/modules/nf-core/samtools/dict/**
 
 samtools/faidx:
-  - modules/nf-core/samtools/faidx/**
-  - tests/modules/nf-core/samtools/faidx/**
+- modules/nf-core/samtools/faidx/**
+- tests/modules/nf-core/samtools/faidx/**
 
 samtools/fasta:
-  - modules/nf-core/samtools/fasta/**
-  - tests/modules/nf-core/samtools/fasta/**
+- modules/nf-core/samtools/fasta/**
+- tests/modules/nf-core/samtools/fasta/**
 
 samtools/fastq:
-  - modules/nf-core/samtools/fastq/**
-  - tests/modules/nf-core/samtools/fastq/**
+- modules/nf-core/samtools/fastq/**
+- tests/modules/nf-core/samtools/fastq/**
 
 samtools/fixmate:
-  - modules/nf-core/samtools/fixmate/**
-  - tests/modules/nf-core/samtools/fixmate/**
+- modules/nf-core/samtools/fixmate/**
+- tests/modules/nf-core/samtools/fixmate/**
 
 samtools/flagstat:
-  - modules/nf-core/samtools/flagstat/**
-  - tests/modules/nf-core/samtools/flagstat/**
+- modules/nf-core/samtools/flagstat/**
+- tests/modules/nf-core/samtools/flagstat/**
 
 samtools/getrg:
-  - modules/nf-core/samtools/getrg/**
-  - tests/modules/nf-core/samtools/getrg/**
+- modules/nf-core/samtools/getrg/**
+- tests/modules/nf-core/samtools/getrg/**
 
 samtools/idxstats:
-  - modules/nf-core/samtools/idxstats/**
-  - tests/modules/nf-core/samtools/idxstats/**
+- modules/nf-core/samtools/idxstats/**
+- tests/modules/nf-core/samtools/idxstats/**
 
 samtools/index:
-  - modules/nf-core/samtools/index/**
-  - tests/modules/nf-core/samtools/index/**
+- modules/nf-core/samtools/index/**
+- tests/modules/nf-core/samtools/index/**
 
 samtools/markdup:
-  - modules/nf-core/samtools/markdup/**
-  - tests/modules/nf-core/samtools/markdup/**
+- modules/nf-core/samtools/markdup/**
+- tests/modules/nf-core/samtools/markdup/**
 
 samtools/merge:
-  - modules/nf-core/samtools/merge/**
-  - tests/modules/nf-core/samtools/merge/**
+- modules/nf-core/samtools/merge/**
+- tests/modules/nf-core/samtools/merge/**
 
 samtools/mpileup:
-  - modules/nf-core/samtools/mpileup/**
-  - tests/modules/nf-core/samtools/mpileup/**
+- modules/nf-core/samtools/mpileup/**
+- tests/modules/nf-core/samtools/mpileup/**
 
 samtools/sort:
-  - modules/nf-core/samtools/sort/**
-  - tests/modules/nf-core/samtools/sort/**
+- modules/nf-core/samtools/sort/**
+- tests/modules/nf-core/samtools/sort/**
 
 samtools/stats:
-  - modules/nf-core/samtools/stats/**
-  - tests/modules/nf-core/samtools/stats/**
+- modules/nf-core/samtools/stats/**
+- tests/modules/nf-core/samtools/stats/**
 
 samtools/view:
-  - modules/nf-core/samtools/view/**
-  - tests/modules/nf-core/samtools/view/**
+- modules/nf-core/samtools/view/**
+- tests/modules/nf-core/samtools/view/**
 
 scoary:
-  - modules/nf-core/scoary/**
-  - tests/modules/nf-core/scoary/**
+- modules/nf-core/scoary/**
+- tests/modules/nf-core/scoary/**
 
 scramble/clusteranalysis:
-  - modules/nf-core/scramble/clusteranalysis/**
-  - tests/modules/nf-core/scramble/clusteranalysis/**
+- modules/nf-core/scramble/clusteranalysis/**
+- tests/modules/nf-core/scramble/clusteranalysis/**
 
 scramble/clusteridentifier:
-  - modules/nf-core/scramble/clusteridentifier/**
-  - tests/modules/nf-core/scramble/clusteridentifier/**
+- modules/nf-core/scramble/clusteridentifier/**
+- tests/modules/nf-core/scramble/clusteridentifier/**
 
 seacr/callpeak:
-  - modules/nf-core/seacr/callpeak/**
-  - tests/modules/nf-core/seacr/callpeak/**
+- modules/nf-core/seacr/callpeak/**
+- tests/modules/nf-core/seacr/callpeak/**
 
 segemehl/align:
-  - modules/nf-core/segemehl/align/**
-  - tests/modules/nf-core/segemehl/align/**
+- modules/nf-core/segemehl/align/**
+- tests/modules/nf-core/segemehl/align/**
 
 segemehl/index:
-  - modules/nf-core/segemehl/index/**
-  - tests/modules/nf-core/segemehl/index/**
+- modules/nf-core/segemehl/index/**
+- tests/modules/nf-core/segemehl/index/**
 
 seqkit/pair:
-  - modules/nf-core/seqkit/pair/**
-  - tests/modules/nf-core/seqkit/pair/**
+- modules/nf-core/seqkit/pair/**
+- tests/modules/nf-core/seqkit/pair/**
 
 seqkit/replace:
-  - modules/nf-core/seqkit/replace/**
-  - tests/modules/nf-core/seqkit/replace/**
+- modules/nf-core/seqkit/replace/**
+- tests/modules/nf-core/seqkit/replace/**
 
 seqkit/split2:
-  - modules/nf-core/seqkit/split2/**
-  - tests/modules/nf-core/seqkit/split2/**
+- modules/nf-core/seqkit/split2/**
+- tests/modules/nf-core/seqkit/split2/**
 
 seqkit/stats:
-  - modules/nf-core/seqkit/stats/**
-  - tests/modules/nf-core/seqkit/stats/**
+- modules/nf-core/seqkit/stats/**
+- tests/modules/nf-core/seqkit/stats/**
 
 seqsero2:
-  - modules/nf-core/seqsero2/**
-  - tests/modules/nf-core/seqsero2/**
+- modules/nf-core/seqsero2/**
+- tests/modules/nf-core/seqsero2/**
 
 seqtk/mergepe:
-  - modules/nf-core/seqtk/mergepe/**
-  - tests/modules/nf-core/seqtk/mergepe/**
+- modules/nf-core/seqtk/mergepe/**
+- tests/modules/nf-core/seqtk/mergepe/**
 
 seqtk/rename:
-  - modules/nf-core/seqtk/rename/**
-  - tests/modules/nf-core/seqtk/rename/**
+- modules/nf-core/seqtk/rename/**
+- tests/modules/nf-core/seqtk/rename/**
 
 seqtk/sample:
-  - modules/nf-core/seqtk/sample/**
-  - tests/modules/nf-core/seqtk/sample/**
+- modules/nf-core/seqtk/sample/**
+- tests/modules/nf-core/seqtk/sample/**
 
 seqtk/seq:
-  - modules/nf-core/seqtk/seq/**
-  - tests/modules/nf-core/seqtk/seq/**
+- modules/nf-core/seqtk/seq/**
+- tests/modules/nf-core/seqtk/seq/**
 
 seqtk/subseq:
-  - modules/nf-core/seqtk/subseq/**
-  - tests/modules/nf-core/seqtk/subseq/**
+- modules/nf-core/seqtk/subseq/**
+- tests/modules/nf-core/seqtk/subseq/**
 
 sequenzautils/bam2seqz:
-  - modules/nf-core/sequenzautils/bam2seqz/**
-  - tests/modules/nf-core/sequenzautils/bam2seqz/**
+- modules/nf-core/sequenzautils/bam2seqz/**
+- tests/modules/nf-core/sequenzautils/bam2seqz/**
 
 sequenzautils/gcwiggle:
-  - modules/nf-core/sequenzautils/gcwiggle/**
-  - tests/modules/nf-core/sequenzautils/gcwiggle/**
+- modules/nf-core/sequenzautils/gcwiggle/**
+- tests/modules/nf-core/sequenzautils/gcwiggle/**
 
 seqwish/induce:
-  - modules/nf-core/seqwish/induce/**
-  - tests/modules/nf-core/seqwish/induce/**
+- modules/nf-core/seqwish/induce/**
+- tests/modules/nf-core/seqwish/induce/**
 
 seroba/run:
-  - modules/nf-core/seroba/run/**
-  - tests/modules/nf-core/seroba/run/**
+- modules/nf-core/seroba/run/**
+- tests/modules/nf-core/seroba/run/**
 
 sexdeterrmine:
-  - modules/nf-core/sexdeterrmine/**
-  - tests/modules/nf-core/sexdeterrmine/**
+- modules/nf-core/sexdeterrmine/**
+- tests/modules/nf-core/sexdeterrmine/**
 
 shasta:
-  - modules/nf-core/shasta/**
-  - tests/modules/nf-core/shasta/**
+- modules/nf-core/shasta/**
+- tests/modules/nf-core/shasta/**
 
 shasum:
-  - modules/nf-core/shasum/**
-  - tests/modules/nf-core/shasum/**
+- modules/nf-core/shasum/**
+- tests/modules/nf-core/shasum/**
 
 shigatyper:
-  - modules/nf-core/shigatyper/**
-  - tests/modules/nf-core/shigatyper/**
+- modules/nf-core/shigatyper/**
+- tests/modules/nf-core/shigatyper/**
 
 shinyngs/app:
-  - modules/nf-core/shinyngs/app/**
-  - tests/modules/nf-core/shinyngs/app/**
+- modules/nf-core/shinyngs/app/**
+- tests/modules/nf-core/shinyngs/app/**
 
 shinyngs/staticexploratory:
-  - modules/nf-core/shinyngs/staticexploratory/**
-  - tests/modules/nf-core/shinyngs/staticexploratory/**
+- modules/nf-core/shinyngs/staticexploratory/**
+- tests/modules/nf-core/shinyngs/staticexploratory/**
 
 shovill:
-  - modules/nf-core/shovill/**
-  - tests/modules/nf-core/shovill/**
+- modules/nf-core/shovill/**
+- tests/modules/nf-core/shovill/**
 
 sistr:
-  - modules/nf-core/sistr/**
-  - tests/modules/nf-core/sistr/**
+- modules/nf-core/sistr/**
+- tests/modules/nf-core/sistr/**
 
 slimfastq:
-  - modules/nf-core/slimfastq/**
-  - tests/modules/nf-core/slimfastq/**
+- modules/nf-core/slimfastq/**
+- tests/modules/nf-core/slimfastq/**
 
 snapaligner/align:
-  - modules/nf-core/snapaligner/align/**
-  - tests/modules/nf-core/snapaligner/align/**
+- modules/nf-core/snapaligner/align/**
+- tests/modules/nf-core/snapaligner/align/**
 
 snapaligner/index:
-  - modules/nf-core/snapaligner/index/**
-  - tests/modules/nf-core/snapaligner/index/**
+- modules/nf-core/snapaligner/index/**
+- tests/modules/nf-core/snapaligner/index/**
 
 snippy/core:
-  - modules/nf-core/snippy/core/**
-  - tests/modules/nf-core/snippy/core/**
+- modules/nf-core/snippy/core/**
+- tests/modules/nf-core/snippy/core/**
 
 snippy/run:
-  - modules/nf-core/snippy/run/**
-  - tests/modules/nf-core/snippy/run/**
+- modules/nf-core/snippy/run/**
+- tests/modules/nf-core/snippy/run/**
 
 snpdists:
-  - modules/nf-core/snpdists/**
-  - tests/modules/nf-core/snpdists/**
+- modules/nf-core/snpdists/**
+- tests/modules/nf-core/snpdists/**
 
 snpeff:
-  - modules/nf-core/snpeff/**
-  - tests/modules/nf-core/snpeff/**
+- modules/nf-core/snpeff/**
+- tests/modules/nf-core/snpeff/**
 
 snpsift/split:
-  - modules/nf-core/snpsift/split/**
-  - tests/modules/nf-core/snpsift/split/**
+- modules/nf-core/snpsift/split/**
+- tests/modules/nf-core/snpsift/split/**
 
 snpsites:
-  - modules/nf-core/snpsites/**
-  - tests/modules/nf-core/snpsites/**
+- modules/nf-core/snpsites/**
+- tests/modules/nf-core/snpsites/**
 
 somalier/extract:
-  - modules/nf-core/somalier/extract/**
-  - tests/modules/nf-core/somalier/extract/**
+- modules/nf-core/somalier/extract/**
+- tests/modules/nf-core/somalier/extract/**
 
 somalier/relate:
-  - modules/nf-core/somalier/relate/**
-  - tests/modules/nf-core/somalier/relate/**
+- modules/nf-core/somalier/relate/**
+- tests/modules/nf-core/somalier/relate/**
 
 sourmash/gather:
-  - modules/nf-core/sourmash/gather/**
-  - tests/modules/nf-core/sourmash/gather/**
+- modules/nf-core/sourmash/gather/**
+- tests/modules/nf-core/sourmash/gather/**
 
 sourmash/sketch:
-  - modules/nf-core/sourmash/sketch/**
-  - tests/modules/nf-core/sourmash/sketch/**
+- modules/nf-core/sourmash/sketch/**
+- tests/modules/nf-core/sourmash/sketch/**
 
 spades:
-  - modules/nf-core/spades/**
-  - tests/modules/nf-core/spades/**
+- modules/nf-core/spades/**
+- tests/modules/nf-core/spades/**
 
 spatyper:
-  - modules/nf-core/spatyper/**
-  - tests/modules/nf-core/spatyper/**
+- modules/nf-core/spatyper/**
+- tests/modules/nf-core/spatyper/**
 
 sratools/fasterqdump:
-  - modules/nf-core/sratools/fasterqdump/**
-  - tests/modules/nf-core/sratools/fasterqdump/**
+- modules/nf-core/sratools/fasterqdump/**
+- tests/modules/nf-core/sratools/fasterqdump/**
 
 sratools/prefetch:
-  - modules/nf-core/sratools/prefetch/**
-  - tests/modules/nf-core/sratools/prefetch/**
+- modules/nf-core/sratools/prefetch/**
+- tests/modules/nf-core/sratools/prefetch/**
 
 srst2/srst2:
-  - modules/nf-core/srst2/srst2/**
-  - tests/modules/nf-core/srst2/srst2/**
+- modules/nf-core/srst2/srst2/**
+- tests/modules/nf-core/srst2/srst2/**
 
 ssuissero:
-  - modules/nf-core/ssuissero/**
-  - tests/modules/nf-core/ssuissero/**
+- modules/nf-core/ssuissero/**
+- tests/modules/nf-core/ssuissero/**
 
 stadeniolib/scramble:
-  - modules/nf-core/stadeniolib/scramble/**
-  - tests/modules/nf-core/stadeniolib/scramble/**
+- modules/nf-core/stadeniolib/scramble/**
+- tests/modules/nf-core/stadeniolib/scramble/**
 
 staphopiasccmec:
-  - modules/nf-core/staphopiasccmec/**
-  - tests/modules/nf-core/staphopiasccmec/**
+- modules/nf-core/staphopiasccmec/**
+- tests/modules/nf-core/staphopiasccmec/**
 
 star/align:
-  - modules/nf-core/star/align/**
-  - tests/modules/nf-core/star/align/**
+- modules/nf-core/star/align/**
+- tests/modules/nf-core/star/align/**
 
 star/genomegenerate:
-  - modules/nf-core/star/genomegenerate/**
-  - tests/modules/nf-core/star/genomegenerate/**
+- modules/nf-core/star/genomegenerate/**
+- tests/modules/nf-core/star/genomegenerate/**
 
 stranger:
-  - modules/nf-core/stranger/**
-  - tests/modules/nf-core/stranger/**
+- modules/nf-core/stranger/**
+- tests/modules/nf-core/stranger/**
 
 strelka/germline:
-  - modules/nf-core/strelka/germline/**
-  - tests/modules/nf-core/strelka/germline/**
+- modules/nf-core/strelka/germline/**
+- tests/modules/nf-core/strelka/germline/**
 
 strelka/somatic:
-  - modules/nf-core/strelka/somatic/**
-  - tests/modules/nf-core/strelka/somatic/**
+- modules/nf-core/strelka/somatic/**
+- tests/modules/nf-core/strelka/somatic/**
 
 stringtie/merge:
-  - modules/nf-core/stringtie/merge/**
-  - tests/modules/nf-core/stringtie/merge/**
+- modules/nf-core/stringtie/merge/**
+- tests/modules/nf-core/stringtie/merge/**
 
 stringtie/stringtie:
-  - modules/nf-core/stringtie/stringtie/**
-  - tests/modules/nf-core/stringtie/stringtie/**
+- modules/nf-core/stringtie/stringtie/**
+- tests/modules/nf-core/stringtie/stringtie/**
 
 subread/featurecounts:
-  - modules/nf-core/subread/featurecounts/**
-  - tests/modules/nf-core/subread/featurecounts/**
+- modules/nf-core/subread/featurecounts/**
+- tests/modules/nf-core/subread/featurecounts/**
 
 subworkflows/align_bowtie2:
-  - subworkflows/nf-core/align_bowtie2/**
-  - tests/subworkflows/nf-core/align_bowtie2/**
+- subworkflows/nf-core/align_bowtie2/**
+- tests/subworkflows/nf-core/align_bowtie2/**
 
 subworkflows/annotation/ensemblvep:
-  - subworkflows/nf-core/annotation/ensemblvep/**
-  - tests/subworkflows/nf-core/annotation/ensemblvep/**
+- subworkflows/nf-core/annotation/ensemblvep/**
+- tests/subworkflows/nf-core/annotation/ensemblvep/**
 
 subworkflows/annotation/snpeff:
-  - subworkflows/nf-core/annotation/snpeff/**
-  - tests/subworkflows/nf-core/annotation/snpeff/**
+- subworkflows/nf-core/annotation/snpeff/**
+- tests/subworkflows/nf-core/annotation/snpeff/**
 
 subworkflows/bam_dedup_stats_samtools_umitools:
-  - subworkflows/nf-core/bam_dedup_stats_samtools_umitools/**
-  - tests/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/**
+- subworkflows/nf-core/bam_dedup_stats_samtools_umitools/**
+- tests/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/**
 
 subworkflows/bam_markduplicates_picard:
-  - subworkflows/nf-core/bam_markduplicates_picard/**
-  - tests/subworkflows/nf-core/bam_markduplicates_picard/**
+- subworkflows/nf-core/bam_markduplicates_picard/**
+- tests/subworkflows/nf-core/bam_markduplicates_picard/**
 
 subworkflows/bam_qc_picard:
-  - subworkflows/nf-core/bam_qc_picard/**
-  - tests/subworkflows/nf-core/bam_qc_picard/**
+- subworkflows/nf-core/bam_qc_picard/**
+- tests/subworkflows/nf-core/bam_qc_picard/**
 
 subworkflows/bam_rseqc:
-  - subworkflows/nf-core/bam_rseqc/**
-  - tests/subworkflows/nf-core/bam_rseqc/**
+- subworkflows/nf-core/bam_rseqc/**
+- tests/subworkflows/nf-core/bam_rseqc/**
 
 subworkflows/bam_sort_samtools:
-  - subworkflows/nf-core/bam_sort_samtools/**
-  - tests/subworkflows/nf-core/bam_sort_samtools/**
+- subworkflows/nf-core/bam_sort_samtools/**
+- tests/subworkflows/nf-core/bam_sort_samtools/**
 
 subworkflows/bam_sort_stats_samtools:
-  - subworkflows/nf-core/bam_sort_stats_samtools/**
-  - tests/subworkflows/nf-core/bam_sort_stats_samtools/**
+- subworkflows/nf-core/bam_sort_stats_samtools/**
+- tests/subworkflows/nf-core/bam_sort_stats_samtools/**
 
 subworkflows/bam_stats_samtools:
-  - subworkflows/nf-core/bam_stats_samtools/**
-  - tests/subworkflows/nf-core/bam_stats_samtools/**
+- subworkflows/nf-core/bam_stats_samtools/**
+- tests/subworkflows/nf-core/bam_stats_samtools/**
 
 subworkflows/bcl_demultiplex:
-  - subworkflows/nf-core/bcl_demultiplex/**
-  - tests/subworkflows/nf-core/bcl_demultiplex/**
+- subworkflows/nf-core/bcl_demultiplex/**
+- tests/subworkflows/nf-core/bcl_demultiplex/**
 
 subworkflows/bedgraph_bedclip_bedgraphtobigwig:
-  - subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/**
-  - tests/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/**
+- subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/**
+- tests/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/**
 
 subworkflows/fasta_index_dna:
-  - subworkflows/nf-core/fasta_index_dna/**
-  - tests/subworkflows/nf-core/fasta_index_dna/**
+- subworkflows/nf-core/fasta_index_dna/**
+- tests/subworkflows/nf-core/fasta_index_dna/**
 
 subworkflows/fastq_align_dna:
-  - subworkflows/nf-core/fastq_align_dna/**
-  - tests/subworkflows/nf-core/fastq_align_dna/**
+- subworkflows/nf-core/fastq_align_dna/**
+- tests/subworkflows/nf-core/fastq_align_dna/**
 
 subworkflows/fastq_align_hisat2:
-  - subworkflows/nf-core/fastq_align_hisat2/**
-  - tests/subworkflows/nf-core/fastq_align_hisat2/**
+- subworkflows/nf-core/fastq_align_hisat2/**
+- tests/subworkflows/nf-core/fastq_align_hisat2/**
 
 subworkflows/fastq_align_star:
-  - subworkflows/nf-core/fastq_align_star/**
-  - tests/subworkflows/nf-core/fastq_align_star/**
+- subworkflows/nf-core/fastq_align_star/**
+- tests/subworkflows/nf-core/fastq_align_star/**
 
 subworkflows/fastq_contam_seqtk_kraken:
-  - subworkflows/nf-core/fastq_contam_seqtk_kraken/**
-  - tests/subworkflows/nf-core/fastq_contam_seqtk_kraken/**
+- subworkflows/nf-core/fastq_contam_seqtk_kraken/**
+- tests/subworkflows/nf-core/fastq_contam_seqtk_kraken/**
 
 subworkflows/fastq_fastqc_umitools_trimgalore:
-  - subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/**
-  - tests/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/**
+- subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/**
+- tests/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/**
 
 subworkflows/gatk_create_som_pon:
-  - subworkflows/nf-core/gatk_create_som_pon/**
-  - tests/subworkflows/nf-core/gatk_create_som_pon/**
+- subworkflows/nf-core/gatk_create_som_pon/**
+- tests/subworkflows/nf-core/gatk_create_som_pon/**
 
 subworkflows/gatk_tumor_normal_somatic_variant_calling:
-  - subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/**
-  - tests/subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/**
+- subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/**
+- tests/subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/**
 
 subworkflows/gatk_tumor_only_somatic_variant_calling:
-  - subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/**
-  - tests/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/**
+- subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/**
+- tests/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/**
 
 subworkflows/homer/groseq:
-  - subworkflows/nf-core/homer/groseq/**
-  - tests/subworkflows/nf-core/homer/groseq/**
+- subworkflows/nf-core/homer/groseq/**
+- tests/subworkflows/nf-core/homer/groseq/**
 
 subworkflows/srafastq:
-  - subworkflows/nf-core/srafastq/**
-  - tests/subworkflows/nf-core/srafastq/**
+- subworkflows/nf-core/srafastq/**
+- tests/subworkflows/nf-core/srafastq/**
 
 svdb/merge:
-  - modules/nf-core/svdb/merge/**
-  - tests/modules/nf-core/svdb/merge/**
+- modules/nf-core/svdb/merge/**
+- tests/modules/nf-core/svdb/merge/**
 
 svdb/query:
-  - modules/nf-core/svdb/query/**
-  - tests/modules/nf-core/svdb/query/**
+- modules/nf-core/svdb/query/**
+- tests/modules/nf-core/svdb/query/**
 
 svtk/baftest:
-  - modules/nf-core/svtk/baftest/**
-  - tests/modules/nf-core/svtk/baftest/**
+- modules/nf-core/svtk/baftest/**
+- tests/modules/nf-core/svtk/baftest/**
 
 svtk/countsvtypes:
-  - modules/nf-core/svtk/countsvtypes/**
-  - tests/modules/nf-core/svtk/countsvtypes/**
+- modules/nf-core/svtk/countsvtypes/**
+- tests/modules/nf-core/svtk/countsvtypes/**
 
 svtk/rdtest2vcf:
-  - modules/nf-core/svtk/rdtest2vcf/**
-  - tests/modules/nf-core/svtk/rdtest2vcf/**
+- modules/nf-core/svtk/rdtest2vcf/**
+- tests/modules/nf-core/svtk/rdtest2vcf/**
 
 svtk/standardize:
-  - modules/nf-core/svtk/standardize/**
-  - tests/modules/nf-core/svtk/standardize/**
+- modules/nf-core/svtk/standardize/**
+- tests/modules/nf-core/svtk/standardize/**
 
 svtk/vcf2bed:
-  - modules/nf-core/svtk/vcf2bed/**
-  - tests/modules/nf-core/svtk/vcf2bed/**
+- modules/nf-core/svtk/vcf2bed/**
+- tests/modules/nf-core/svtk/vcf2bed/**
 
 tabix/bgzip:
-  - modules/nf-core/tabix/bgzip/**
-  - tests/modules/nf-core/tabix/bgzip/**
+- modules/nf-core/tabix/bgzip/**
+- tests/modules/nf-core/tabix/bgzip/**
 
 tabix/bgziptabix:
-  - modules/nf-core/tabix/bgziptabix/**
-  - tests/modules/nf-core/tabix/bgziptabix/**
+- modules/nf-core/tabix/bgziptabix/**
+- tests/modules/nf-core/tabix/bgziptabix/**
 
 tabix/tabix:
-  - modules/nf-core/tabix/tabix/**
-  - tests/modules/nf-core/tabix/tabix/**
+- modules/nf-core/tabix/tabix/**
+- tests/modules/nf-core/tabix/tabix/**
 
 tailfindr:
-  - modules/nf-core/tailfindr/**
-  - tests/modules/nf-core/tailfindr/**
+- modules/nf-core/tailfindr/**
+- tests/modules/nf-core/tailfindr/**
 
 tbprofiler/profile:
-  - modules/nf-core/tbprofiler/profile/**
-  - tests/modules/nf-core/tbprofiler/profile/**
+- modules/nf-core/tbprofiler/profile/**
+- tests/modules/nf-core/tbprofiler/profile/**
 
 tiddit/cov:
-  - modules/nf-core/tiddit/cov/**
-  - tests/modules/nf-core/tiddit/cov/**
+- modules/nf-core/tiddit/cov/**
+- tests/modules/nf-core/tiddit/cov/**
 
 tiddit/sv:
-  - modules/nf-core/tiddit/sv/**
-  - tests/modules/nf-core/tiddit/sv/**
+- modules/nf-core/tiddit/sv/**
+- tests/modules/nf-core/tiddit/sv/**
 
 transdecoder/longorf:
-  - modules/nf-core/transdecoder/longorf/**
-  - tests/modules/nf-core/transdecoder/longorf/**
+- modules/nf-core/transdecoder/longorf/**
+- tests/modules/nf-core/transdecoder/longorf/**
 
 transdecoder/predict:
-  - modules/nf-core/transdecoder/predict/**
-  - tests/modules/nf-core/transdecoder/predict/**
+- modules/nf-core/transdecoder/predict/**
+- tests/modules/nf-core/transdecoder/predict/**
 
 trimgalore:
-  - modules/nf-core/trimgalore/**
-  - tests/modules/nf-core/trimgalore/**
+- modules/nf-core/trimgalore/**
+- tests/modules/nf-core/trimgalore/**
 
 trimmomatic:
-  - modules/nf-core/trimmomatic/**
-  - tests/modules/nf-core/trimmomatic/**
+- modules/nf-core/trimmomatic/**
+- tests/modules/nf-core/trimmomatic/**
 
 ucsc/bedclip:
-  - modules/nf-core/ucsc/bedclip/**
-  - tests/modules/nf-core/ucsc/bedclip/**
+- modules/nf-core/ucsc/bedclip/**
+- tests/modules/nf-core/ucsc/bedclip/**
 
 ucsc/bedgraphtobigwig:
-  - modules/nf-core/ucsc/bedgraphtobigwig/**
-  - tests/modules/nf-core/ucsc/bedgraphtobigwig/**
+- modules/nf-core/ucsc/bedgraphtobigwig/**
+- tests/modules/nf-core/ucsc/bedgraphtobigwig/**
 
 ucsc/bedtobigbed:
-  - modules/nf-core/ucsc/bedtobigbed/**
-  - tests/modules/nf-core/ucsc/bedtobigbed/**
+- modules/nf-core/ucsc/bedtobigbed/**
+- tests/modules/nf-core/ucsc/bedtobigbed/**
 
 ucsc/bigwigaverageoverbed:
-  - modules/nf-core/ucsc/bigwigaverageoverbed/**
-  - tests/modules/nf-core/ucsc/bigwigaverageoverbed/**
+- modules/nf-core/ucsc/bigwigaverageoverbed/**
+- tests/modules/nf-core/ucsc/bigwigaverageoverbed/**
 
 ucsc/gtftogenepred:
-  - modules/nf-core/ucsc/gtftogenepred/**
-  - tests/modules/nf-core/ucsc/gtftogenepred/**
+- modules/nf-core/ucsc/gtftogenepred/**
+- tests/modules/nf-core/ucsc/gtftogenepred/**
 
 ucsc/liftover:
-  - modules/nf-core/ucsc/liftover/**
-  - tests/modules/nf-core/ucsc/liftover/**
+- modules/nf-core/ucsc/liftover/**
+- tests/modules/nf-core/ucsc/liftover/**
 
 ucsc/wigtobigwig:
-  - modules/nf-core/ucsc/wigtobigwig/**
-  - tests/modules/nf-core/ucsc/wigtobigwig/**
+- modules/nf-core/ucsc/wigtobigwig/**
+- tests/modules/nf-core/ucsc/wigtobigwig/**
 
 ultra/align:
-  - modules/nf-core/ultra/align/**
-  - tests/modules/nf-core/ultra/align/**
+- modules/nf-core/ultra/align/**
+- tests/modules/nf-core/ultra/align/**
 
 ultra/index:
-  - modules/nf-core/ultra/index/**
-  - tests/modules/nf-core/ultra/index/**
+- modules/nf-core/ultra/index/**
+- tests/modules/nf-core/ultra/index/**
 
 ultra/pipeline:
-  - modules/nf-core/ultra/pipeline/**
-  - tests/modules/nf-core/ultra/pipeline/**
+- modules/nf-core/ultra/pipeline/**
+- tests/modules/nf-core/ultra/pipeline/**
 
 umitools/dedup:
-  - modules/nf-core/umitools/dedup/**
-  - modules/nf-core/umitools/extract/**
-  - tests/modules/nf-core/umitools/dedup/**
+- modules/nf-core/umitools/dedup/**
+- modules/nf-core/umitools/extract/**
+- tests/modules/nf-core/umitools/dedup/**
 
 umitools/extract:
-  - modules/nf-core/umitools/extract/**
-  - tests/modules/nf-core/umitools/extract/**
+- modules/nf-core/umitools/extract/**
+- tests/modules/nf-core/umitools/extract/**
 
 unicycler:
-  - modules/nf-core/unicycler/**
-  - tests/modules/nf-core/unicycler/**
+- modules/nf-core/unicycler/**
+- tests/modules/nf-core/unicycler/**
 
 untar:
-  - modules/nf-core/untar/**
-  - tests/modules/nf-core/untar/**
+- modules/nf-core/untar/**
+- tests/modules/nf-core/untar/**
 
 unzip:
-  - modules/nf-core/unzip/**
-  - tests/modules/nf-core/unzip/**
+- modules/nf-core/unzip/**
+- tests/modules/nf-core/unzip/**
 
 vardictjava:
-  - modules/nf-core/vardictjava/**
-  - tests/modules/nf-core/vardictjava/**
+- modules/nf-core/vardictjava/**
+- tests/modules/nf-core/vardictjava/**
 
 variantbam:
-  - modules/nf-core/variantbam/**
-  - tests/modules/nf-core/variantbam/**
+- modules/nf-core/variantbam/**
+- tests/modules/nf-core/variantbam/**
 
 vcf2db:
-  - modules/nf-core/vcf2db/**
-  - tests/modules/nf-core/vcf2db/**
+- modules/nf-core/vcf2db/**
+- tests/modules/nf-core/vcf2db/**
 
 vcf2maf:
-  - modules/nf-core/vcf2maf/**
-  - tests/modules/nf-core/vcf2maf/**
+- modules/nf-core/vcf2maf/**
+- tests/modules/nf-core/vcf2maf/**
 
 vcfanno:
-  - modules/nf-core/vcfanno/**
-  - tests/modules/nf-core/vcfanno/**
+- modules/nf-core/vcfanno/**
+- tests/modules/nf-core/vcfanno/**
 
 vcflib/vcfbreakmulti:
-  - modules/nf-core/vcflib/vcfbreakmulti/**
-  - tests/modules/nf-core/vcflib/vcfbreakmulti/**
+- modules/nf-core/vcflib/vcfbreakmulti/**
+- tests/modules/nf-core/vcflib/vcfbreakmulti/**
 
 vcflib/vcfuniq:
-  - modules/nf-core/vcflib/vcfuniq/**
-  - tests/modules/nf-core/vcflib/vcfuniq/**
+- modules/nf-core/vcflib/vcfuniq/**
+- tests/modules/nf-core/vcflib/vcfuniq/**
 
 vcftools:
-  - modules/nf-core/vcftools/**
-  - tests/modules/nf-core/vcftools/**
+- modules/nf-core/vcftools/**
+- tests/modules/nf-core/vcftools/**
 
 verifybamid/verifybamid2:
-  - modules/nf-core/verifybamid/verifybamid2/**
-  - tests/modules/nf-core/verifybamid/verifybamid2/**
+- modules/nf-core/verifybamid/verifybamid2/**
+- tests/modules/nf-core/verifybamid/verifybamid2/**
 
 vg/deconstruct:
-  - modules/nf-core/vg/deconstruct/**
-  - tests/modules/nf-core/vg/deconstruct/**
+- modules/nf-core/vg/deconstruct/**
+- tests/modules/nf-core/vg/deconstruct/**
 
 vsearch/cluster:
-  - modules/nf-core/vsearch/cluster/**
-  - tests/modules/nf-core/vsearch/cluster/**
+- modules/nf-core/vsearch/cluster/**
+- tests/modules/nf-core/vsearch/cluster/**
 
 vsearch/sintax:
-  - modules/nf-core/vsearch/sintax/**
-  - tests/modules/nf-core/vsearch/sintax/**
+- modules/nf-core/vsearch/sintax/**
+- tests/modules/nf-core/vsearch/sintax/**
 
 vsearch/usearchglobal:
-  - modules/nf-core/vsearch/usearchglobal/**
-  - tests/modules/nf-core/vsearch/usearchglobal/**
+- modules/nf-core/vsearch/usearchglobal/**
+- tests/modules/nf-core/vsearch/usearchglobal/**
 
 wgsim:
-  - modules/nf-core/wgsim/**
-  - tests/modules/nf-core/wgsim/**
+- modules/nf-core/wgsim/**
+- tests/modules/nf-core/wgsim/**
 
 whamg:
-  - modules/nf-core/whamg/**
-  - tests/modules/nf-core/whamg/**
+- modules/nf-core/whamg/**
+- tests/modules/nf-core/whamg/**
 
 yara/index:
-  - modules/nf-core/yara/index/**
-  - tests/modules/nf-core/yara/index/**
+- modules/nf-core/yara/index/**
+- tests/modules/nf-core/yara/index/**
 
 yara/mapper:
-  - modules/nf-core/yara/mapper/**
-  - tests/modules/nf-core/yara/mapper/**
+- modules/nf-core/yara/mapper/**
+- tests/modules/nf-core/yara/mapper/**

From 715a1c4b046f11efde49030654362381f2f3a0e7 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Tue, 1 Nov 2022 09:58:50 -0400
Subject: [PATCH 002/114] added default output filename.

---
 modules/nf-core/ashlar/ashlar.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/nf-core/ashlar/ashlar.nf b/modules/nf-core/ashlar/ashlar.nf
index 540708919e9..99f2e594287 100644
--- a/modules/nf-core/ashlar/ashlar.nf
+++ b/modules/nf-core/ashlar/ashlar.nf
@@ -68,6 +68,7 @@ process wc {
 
 process ashlar {
     conda 'bioconda::ashlar=1.17.0'
+    params.out = 'ashlar_output.ome.tif'
 
     input:
         path file_in

From 10f20541f23b9061c706349dca5e8398bf8ff68d Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Tue, 1 Nov 2022 10:21:18 -0400
Subject: [PATCH 003/114] changed output parameter to match ashlar param name
 and changed output path to allow for both output file types

---
 modules/nf-core/ashlar/ashlar.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/nf-core/ashlar/ashlar.nf b/modules/nf-core/ashlar/ashlar.nf
index 99f2e594287..34d1e063e3e 100644
--- a/modules/nf-core/ashlar/ashlar.nf
+++ b/modules/nf-core/ashlar/ashlar.nf
@@ -68,15 +68,15 @@ process wc {
 
 process ashlar {
     conda 'bioconda::ashlar=1.17.0'
-    params.out = 'ashlar_output.ome.tif'
+    params.output = 'ashlar_output.ome.tif'
 
     input:
         path file_in
     output:
-        path '*.ome.tif'
+        path '*.tif'
 
     """
-    ashlar $file_in -o $params.out
+    ashlar $file_in -o $params.output
     """
 
 }

From 91b8e3a3954322e5fb3fe8fce9380a74c13d4576 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Tue, 1 Nov 2022 10:28:01 -0400
Subject: [PATCH 004/114] added optional input parameter channel

---
 modules/nf-core/ashlar/ashlar.nf | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/ashlar/ashlar.nf b/modules/nf-core/ashlar/ashlar.nf
index 34d1e063e3e..f71e265cbdf 100644
--- a/modules/nf-core/ashlar/ashlar.nf
+++ b/modules/nf-core/ashlar/ashlar.nf
@@ -69,6 +69,7 @@ process wc {
 process ashlar {
     conda 'bioconda::ashlar=1.17.0'
     params.output = 'ashlar_output.ome.tif'
+    params.channel = '0'
 
     input:
         path file_in
@@ -76,7 +77,7 @@ process ashlar {
         path '*.tif'
 
     """
-    ashlar $file_in -o $params.output
+    ashlar $file_in -o $params.output -c $params.channel
     """
 
 }

From e09d8ad5e3e72038255454557f058b591d6d6755 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Tue, 1 Nov 2022 16:26:16 -0400
Subject: [PATCH 005/114] added most input paramters. working code

---
 modules/nf-core/ashlar/ashlar.nf | 51 +++++++++++++++++++++++++++++---
 1 file changed, 47 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/ashlar/ashlar.nf b/modules/nf-core/ashlar/ashlar.nf
index f71e265cbdf..5cda84f9c24 100644
--- a/modules/nf-core/ashlar/ashlar.nf
+++ b/modules/nf-core/ashlar/ashlar.nf
@@ -70,16 +70,59 @@ process ashlar {
     conda 'bioconda::ashlar=1.17.0'
     params.output = 'ashlar_output.ome.tif'
     params.channel = '0'
+    params.flip_x = ''
+    params.flip_y = ''
+    params.flip_mosaic_x = ''
+    params.flip_mosaic_y = ''
+    params.maximum_shift = '15'
+    params.filter_sigma = ''
+    params.tile_size = '1024'
+    params.plates = ''
+    params.quiet = ''
+    params.help = ''
+    params.version = ''
 
     input:
         path file_in
     output:
         path '*.tif'
 
-    """
-    ashlar $file_in -o $params.output -c $params.channel
-    """
-
+    script:
+    def flip_x = params.flip_x == '' ? '' : '--flip-x'
+    def flip_y = params.flip_y == '' ? '' : '--flip-y'
+    def flip_mosaic_x = params.flip_mosaic_x == '' ? '' : '--flip-mosaic-x'
+    def flip_mosaic_y = params.flip_mosaic_y == '' ? '' : '--flip-mosaic-y'
+    def filter_sigma = params.filter_sigma == '' ? '' : '--filter-sigma ' + params.filter_sigma
+    def plates = params.plates == '' ? '' : '--plates'
+    def quiet = params.quiet == '' ? '' : '--quiet'
+    def help = params.help == '' ? false : true
+    def version = params.version == '' ? false : true
+
+    if(!help && !version) {
+        """
+        ashlar $file_in -o $params.output -c $params.channel $flip_x $flip_y $flip_mosaic_x $flip_mosaic_y -m $params.maximum_shift $filter_sigma --tile-size $params.tile_size $plates $quiet
+        """
+    }
+    else if(help && version) {
+        """
+        echo 'Please select either the help or version input parameter, but not both.'
+        """
+    }
+    else if(help) {
+        """
+        ashlar --help
+        """
+    }
+    else if(version) {
+        """
+        ashlar --version
+        """
+    }
+    else {
+        """
+        ashlar --help
+        """
+    }
 }
 
 workflow {

From 84269e4000bc36b89616f69aea83cd85d9cb1b2d Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Tue, 1 Nov 2022 16:45:09 -0400
Subject: [PATCH 006/114] clean-up

---
 modules/nf-core/ashlar/ashlar.nf | 60 --------------------------------
 1 file changed, 60 deletions(-)

diff --git a/modules/nf-core/ashlar/ashlar.nf b/modules/nf-core/ashlar/ashlar.nf
index 5cda84f9c24..a3e433419f7 100644
--- a/modules/nf-core/ashlar/ashlar.nf
+++ b/modules/nf-core/ashlar/ashlar.nf
@@ -1,60 +1,3 @@
-params.str = 'Hello world!'
-
-process splitLetters {
-  output:
-    path 'chunk_*'
-
-  """
-  printf '${params.str}' | split -b 6 - chunk_
-  """
-}
-
-process convertToUpper {
-  input:
-    path x
-  output:
-    stdout
-
-  """
-  cat $x | tr '[a-z]' '[A-Z]'
-  """
-}
-
-process ashlar_works_1 {
-    conda 'bioconda::ashlar=1.17.0'
-
-    input:
-        path file_in
-    output:
-        stdout
-
-    """
-    ashlar $file_in -o foo.ome.tif
-    """
-
-    /*
-    output:
-        stdout
-    """
-    ashlar --help
-    """
-    */
-}
-
-process ashlar_works_2 {
-    conda 'bioconda::ashlar=1.17.0'
-
-    input:
-        path file_in
-    output:
-        stdout
-
-    """
-    ashlar $file_in -o $params.out
-    """
-
-}
-
 process wc {
     input:
         path file_in
@@ -126,8 +69,5 @@ process ashlar {
 }
 
 workflow {
-  // splitLetters | flatten | convertToUpper | view { it.trim() }
-  // ashlar(params.in) | view { it.trim() }
-  //wc(params.in) | view { it.trim() }
   ashlar(params.in) | wc | view { it.trim() }
 }

From 724412e0cf24727b261fe0e1c26b26ea02589a21 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Tue, 1 Nov 2022 17:12:13 -0400
Subject: [PATCH 007/114] added output-channels parameter

---
 modules/nf-core/ashlar/ashlar.nf | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/ashlar/ashlar.nf b/modules/nf-core/ashlar/ashlar.nf
index a3e433419f7..9b93854a9dd 100644
--- a/modules/nf-core/ashlar/ashlar.nf
+++ b/modules/nf-core/ashlar/ashlar.nf
@@ -24,6 +24,7 @@ process ashlar {
     params.quiet = ''
     params.help = ''
     params.version = ''
+    params.output_channels = ''
 
     input:
         path file_in
@@ -31,6 +32,7 @@ process ashlar {
         path '*.tif'
 
     script:
+    println file_in
     def flip_x = params.flip_x == '' ? '' : '--flip-x'
     def flip_y = params.flip_y == '' ? '' : '--flip-y'
     def flip_mosaic_x = params.flip_mosaic_x == '' ? '' : '--flip-mosaic-x'
@@ -40,10 +42,11 @@ process ashlar {
     def quiet = params.quiet == '' ? '' : '--quiet'
     def help = params.help == '' ? false : true
     def version = params.version == '' ? false : true
+    def output_channels = params.output_channels == '' ? '' : '--output-channels ' + params.output_channels
 
     if(!help && !version) {
         """
-        ashlar $file_in -o $params.output -c $params.channel $flip_x $flip_y $flip_mosaic_x $flip_mosaic_y -m $params.maximum_shift $filter_sigma --tile-size $params.tile_size $plates $quiet
+        ashlar $file_in -o $params.output -c $params.channel $flip_x $flip_y $flip_mosaic_x $flip_mosaic_y -m $params.maximum_shift $filter_sigma --tile-size $params.tile_size $plates $quiet $output_channels
         """
     }
     else if(help && version) {

From 62e16c6be33030e3b93aea503b199db034250a54 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Wed, 2 Nov 2022 09:59:50 -0400
Subject: [PATCH 008/114] added support for multiple input files

---
 modules/nf-core/ashlar/ashlar.nf | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/ashlar/ashlar.nf b/modules/nf-core/ashlar/ashlar.nf
index 9b93854a9dd..45d8ceb3918 100644
--- a/modules/nf-core/ashlar/ashlar.nf
+++ b/modules/nf-core/ashlar/ashlar.nf
@@ -32,7 +32,6 @@ process ashlar {
         path '*.tif'
 
     script:
-    println file_in
     def flip_x = params.flip_x == '' ? '' : '--flip-x'
     def flip_y = params.flip_y == '' ? '' : '--flip-y'
     def flip_mosaic_x = params.flip_mosaic_x == '' ? '' : '--flip-mosaic-x'
@@ -72,5 +71,7 @@ process ashlar {
 }
 
 workflow {
-  ashlar(params.in) | wc | view { it.trim() }
+    input_file_list = params.in.split(',') as List
+    ch_input_files = Channel.fromList( input_file_list )
+    ashlar(ch_input_files) | wc | view {it.trim() }
 }

From ccdc22d87084db57074cb6f0243a6451ed92751a Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Wed, 2 Nov 2022 14:10:16 -0400
Subject: [PATCH 009/114] added ffp input parameter

---
 modules/nf-core/ashlar/ashlar.nf | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/ashlar/ashlar.nf b/modules/nf-core/ashlar/ashlar.nf
index 45d8ceb3918..4780581b201 100644
--- a/modules/nf-core/ashlar/ashlar.nf
+++ b/modules/nf-core/ashlar/ashlar.nf
@@ -25,9 +25,11 @@ process ashlar {
     params.help = ''
     params.version = ''
     params.output_channels = ''
+    params.ffp = ''
 
     input:
         path file_in
+        val file_ffp
     output:
         path '*.tif'
 
@@ -42,10 +44,11 @@ process ashlar {
     def help = params.help == '' ? false : true
     def version = params.version == '' ? false : true
     def output_channels = params.output_channels == '' ? '' : '--output-channels ' + params.output_channels
+    def ffp = params.ffp == '' ? '' : '--ffp ' + file_ffp
 
     if(!help && !version) {
         """
-        ashlar $file_in -o $params.output -c $params.channel $flip_x $flip_y $flip_mosaic_x $flip_mosaic_y -m $params.maximum_shift $filter_sigma --tile-size $params.tile_size $plates $quiet $output_channels
+        ashlar $file_in -o $params.output -c $params.channel $flip_x $flip_y $flip_mosaic_x $flip_mosaic_y -m $params.maximum_shift $filter_sigma --tile-size $params.tile_size $plates $quiet $output_channels $ffp
         """
     }
     else if(help && version) {
@@ -73,5 +76,16 @@ process ashlar {
 workflow {
     input_file_list = params.in.split(',') as List
     ch_input_files = Channel.fromList( input_file_list )
-    ashlar(ch_input_files) | wc | view {it.trim() }
+    def ffp_file_list = []
+    if(params.ffp) {
+        ffp_file_list = params.ffp.split(',') as List
+        ch_ffp_files = Channel.fromList( ffp_file_list )
+    }
+    else {
+        for(item in input_file_list){
+            ffp_file_list.add('/dev/null')
+        }
+        ch_ffp_files = Channel.fromList (ffp_file_list)
+    }
+    ashlar(ch_input_files, ch_ffp_files) | wc | view { it.trim() }
 }

From b4178e74c94f973973a2973e23b63286277df8d2 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Wed, 2 Nov 2022 16:02:26 -0400
Subject: [PATCH 010/114] bug fix: should not have had multiple channels

---
 modules/nf-core/ashlar/ashlar.nf | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/modules/nf-core/ashlar/ashlar.nf b/modules/nf-core/ashlar/ashlar.nf
index 4780581b201..9e763ce91ab 100644
--- a/modules/nf-core/ashlar/ashlar.nf
+++ b/modules/nf-core/ashlar/ashlar.nf
@@ -26,10 +26,12 @@ process ashlar {
     params.version = ''
     params.output_channels = ''
     params.ffp = ''
+    params.dfp = ''
 
     input:
-        path file_in
+        val file_in
         val file_ffp
+        val file_dfp
     output:
         path '*.tif'
 
@@ -45,10 +47,11 @@ process ashlar {
     def version = params.version == '' ? false : true
     def output_channels = params.output_channels == '' ? '' : '--output-channels ' + params.output_channels
     def ffp = params.ffp == '' ? '' : '--ffp ' + file_ffp
+    def dfp = params.dfp == '' ? '' : '--dfp ' + file_dfp
 
     if(!help && !version) {
         """
-        ashlar $file_in -o $params.output -c $params.channel $flip_x $flip_y $flip_mosaic_x $flip_mosaic_y -m $params.maximum_shift $filter_sigma --tile-size $params.tile_size $plates $quiet $output_channels $ffp
+        ashlar $file_in -o $params.output -c $params.channel $flip_x $flip_y $flip_mosaic_x $flip_mosaic_y -m $params.maximum_shift $filter_sigma --tile-size $params.tile_size $plates $quiet $output_channels $ffp $dfp
         """
     }
     else if(help && version) {
@@ -74,18 +77,15 @@ process ashlar {
 }
 
 workflow {
-    input_file_list = params.in.split(',') as List
-    ch_input_files = Channel.fromList( input_file_list )
-    def ffp_file_list = []
+    input_file_list = params.in.split(',').join(' ')
+    ffp_file_list = []
     if(params.ffp) {
-        ffp_file_list = params.ffp.split(',') as List
-        ch_ffp_files = Channel.fromList( ffp_file_list )
+        ffp_file_list = params.ffp.split(',').join(' ')
     }
-    else {
-        for(item in input_file_list){
-            ffp_file_list.add('/dev/null')
-        }
-        ch_ffp_files = Channel.fromList (ffp_file_list)
+    dfp_file_list = []
+    if(params.dfp) {
+        dfp_file_list = params.dfp.split(',').join(' ')
     }
-    ashlar(ch_input_files, ch_ffp_files) | wc | view { it.trim() }
+
+    ashlar(input_file_list, ffp_file_list, dfp_file_list) | wc | view { it.trim() }
 }

From 11ee7b8f0eb00334da2fb7da2e19708f7536227e Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Thu, 3 Nov 2022 17:11:30 -0400
Subject: [PATCH 011/114] most of meta.yml filled out. still need the case for
 *.tif output

---
 modules/nf-core/ashlar/meta.yml | 37 +++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 modules/nf-core/ashlar/meta.yml

diff --git a/modules/nf-core/ashlar/meta.yml b/modules/nf-core/ashlar/meta.yml
new file mode 100644
index 00000000000..05c064c0ce8
--- /dev/null
+++ b/modules/nf-core/ashlar/meta.yml
@@ -0,0 +1,37 @@
+name: "ashlar"
+description: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration
+keywords:
+  - image processing, alignment, registration
+tools:
+  #
+  - "ashlar":
+      description: "Alignment by Simultaneous Harmonization of Layer/Adjacency Registration"
+      homepage: "https://labsyspharm.github.io/ashlar/"
+      documentation: "https://labsyspharm.github.io/ashlar/"
+      tool_dev_url: "None"
+      doi: "10.1101/2021.04.20.440625"
+      licence: "['MIT']"
+
+input:
+  #
+  - file_in:
+      type: file
+      description: multidimentional image data in formats from most commercial microscopes
+      pattern: "*.ome.tiff"
+
+output:
+  #
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  ## TODO nf-core: This just handles one output option.  We also have to handle the case
+  ##               where the user requests a series of single-channel plain TIFF files
+  ##               by setting the output filename to *.tif
+  - file_out:
+      type: file
+      description: pyramidal OME-TIFF
+      pattern: "*.ome.tif"
+
+authors:
+  - "@RobJY"

From 7e20a5d6d15b7122eccbe605be085b0e0c5d49ab Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Thu, 3 Nov 2022 17:20:42 -0400
Subject: [PATCH 012/114] ah, also need to add defaults and optional args to
 meta.yml

---
 modules/nf-core/ashlar/meta.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/nf-core/ashlar/meta.yml b/modules/nf-core/ashlar/meta.yml
index 05c064c0ce8..5c31c64b701 100644
--- a/modules/nf-core/ashlar/meta.yml
+++ b/modules/nf-core/ashlar/meta.yml
@@ -14,6 +14,7 @@ tools:
 
 input:
   #
+  ## TODO nf-core: need to add optional and default parameters
   - file_in:
       type: file
       description: multidimentional image data in formats from most commercial microscopes

From c85d04d3342bdbdf314387b6600f2048ccafbe7d Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Thu, 3 Nov 2022 17:36:09 -0400
Subject: [PATCH 013/114] minimal set of input parameters added to meta.yml for
 testing; need to set defaults for them

---
 modules/nf-core/ashlar/meta.yml | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/ashlar/meta.yml b/modules/nf-core/ashlar/meta.yml
index 5c31c64b701..343ad50f3fa 100644
--- a/modules/nf-core/ashlar/meta.yml
+++ b/modules/nf-core/ashlar/meta.yml
@@ -1,7 +1,7 @@
 name: "ashlar"
 description: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration
 keywords:
-  - image processing, alignment, registration
+  - image_processing, alignment, registration
 tools:
   #
   - "ashlar":
@@ -19,6 +19,18 @@ input:
       type: file
       description: multidimentional image data in formats from most commercial microscopes
       pattern: "*.ome.tiff"
+  - align_channel:
+      type: integer
+      description: Reference channel number for image alignment. Numbering starts at 0. (default: 0)
+      ## TODO nf-core: how do we set a default
+  - maximum-shift:
+      type: integer
+      description: Maximum allowed per-tile corrective shift in microns (default: 15)
+      ## TODO nf-core: need to set default
+  - tile_size:
+      type: integer
+      description: Pyramid tile size for OME-TIFF output (default: 1024)
+      ## TODO nf-core: need to set default
 
 output:
   #

From 2a8ea15fd596bbda21adf722d16d01ba2268ed31 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Mon, 14 Nov 2022 14:19:16 -0500
Subject: [PATCH 014/114] runs simple test with hard-coded paths

---
 modules/nf-core/ashlar/ashlar.nf |  1 +
 modules/nf-core/ashlar/meta.yml  | 12 ------------
 2 files changed, 1 insertion(+), 12 deletions(-)

diff --git a/modules/nf-core/ashlar/ashlar.nf b/modules/nf-core/ashlar/ashlar.nf
index 9e763ce91ab..7e047d890aa 100644
--- a/modules/nf-core/ashlar/ashlar.nf
+++ b/modules/nf-core/ashlar/ashlar.nf
@@ -10,6 +10,7 @@ process wc {
 }
 
 process ashlar {
+    println 'running process ashlar in ashlar.nf'
     conda 'bioconda::ashlar=1.17.0'
     params.output = 'ashlar_output.ome.tif'
     params.channel = '0'
diff --git a/modules/nf-core/ashlar/meta.yml b/modules/nf-core/ashlar/meta.yml
index 343ad50f3fa..d0f68c23771 100644
--- a/modules/nf-core/ashlar/meta.yml
+++ b/modules/nf-core/ashlar/meta.yml
@@ -19,18 +19,6 @@ input:
       type: file
       description: multidimentional image data in formats from most commercial microscopes
       pattern: "*.ome.tiff"
-  - align_channel:
-      type: integer
-      description: Reference channel number for image alignment. Numbering starts at 0. (default: 0)
-      ## TODO nf-core: how do we set a default
-  - maximum-shift:
-      type: integer
-      description: Maximum allowed per-tile corrective shift in microns (default: 15)
-      ## TODO nf-core: need to set default
-  - tile_size:
-      type: integer
-      description: Pyramid tile size for OME-TIFF output (default: 1024)
-      ## TODO nf-core: need to set default
 
 output:
   #

From 68e41896434c5b2ca63e16031f1f3fc7dcc8902b Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Mon, 14 Nov 2022 14:37:21 -0500
Subject: [PATCH 015/114] simple test works with input parameter and no
 hard-coded paths

---
 tests/modules/nf-core/ashlar/main.nf | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 tests/modules/nf-core/ashlar/main.nf

diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
new file mode 100644
index 00000000000..eb0db7f3b42
--- /dev/null
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -0,0 +1,22 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ASHLAR } from '../../../../../modules/modules/nf-core/ashlar/main.nf'
+
+workflow test_ashlar {
+
+    println 'running workflow test_ashlar'
+
+    /*
+    // TO DO: test with input sample sheet like the following
+    input = file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)=
+    ASHLAR ( input )
+    */
+
+    // input_channel = Channel.fromPath( '/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-06.ome.tiff' )
+    input_channel = Channel.fromPath( params.file_in )
+    ASHLAR ( input_channel )
+
+    //ASHLAR ( file('/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-06.ome.tiff') )
+}

From 6ad6999d9d8f7e76dacef1bc944f2f07a9e7af54 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Mon, 14 Nov 2022 14:38:12 -0500
Subject: [PATCH 016/114] added ashlar main module file

---
 modules/nf-core/ashlar/main.nf | 92 ++++++++++++++++++++++++++++++++++
 1 file changed, 92 insertions(+)
 create mode 100644 modules/nf-core/ashlar/main.nf

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
new file mode 100644
index 00000000000..b50940478ba
--- /dev/null
+++ b/modules/nf-core/ashlar/main.nf
@@ -0,0 +1,92 @@
+// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
+//               https://github.com/nf-core/modules/tree/master/modules
+//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
+//               https://nf-co.re/join
+// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
+//               All other parameters MUST be provided using the "task.ext" directive, see here:
+//               https://www.nextflow.io/docs/latest/process.html#ext
+//               where "task.ext" is a string.
+//               Any parameters that need to be evaluated in the context of a particular sample
+//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
+// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
+//               unless there is a run-time, storage advantage in implementing in this way
+//               e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
+//                 bwa mem | samtools view -B -T ref.fasta
+// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
+//               list (`[]`) instead of a file can be used to work around this issue.
+
+println 'running main.nf'
+
+process ASHLAR {
+    println 'running process ASHLAR'
+
+    tag '$file_in'
+    label 'process_single'
+
+    // TODO nf-core: List required Conda package(s).
+    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
+    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
+    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
+    // TODO nf-core: need versions for all packages below
+    //conda (params.enable_conda ? "bioconda::ashlar=1.17.0" : null)
+    conda "bioconda::ashlar=1.17.0"
+
+    /*
+    TODO nf-core: how do we referene that we'll
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE':
+        'quay.io/biocontainers/YOUR-TOOL-HERE' }"
+    */
+    //container "/home/pollen/github/modules/modules/nf-core/ashlar/ashlar.img"
+
+    input:
+    // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
+    //               MUST be provided as an input via a Groovy Map called "meta".
+    //               This information may not be required in some instances e.g. indexing reference genome files:
+    //               https://github.com/nf-core/modules/blob/master/modules/bwa/index/main.nf
+    // TODO nf-core: Where applicable please provide/convert compressed files as input/output
+    //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
+    path file_in
+
+    output:
+    // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
+    // TODO nf-core: List additional required output channels/values here
+    path "*.ome.tif"
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    //def args = task.ext.args ?: ''
+
+    // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
+    //               If the software is unable to output a version number on the command-line then it can be manually specified
+    //               e.g. https://github.com/nf-core/modules/blob/master/modules/homer/annotatepeaks/main.nf
+    //               Each software used MUST provide the software name and version number in the YAML version file (versions.yml)
+    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
+    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
+    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
+    // TODO nf-core: Please replace the example samtools command below with your module's command
+    // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
+
+    /*
+    ashlar \\
+        $file_in \\
+        $args \\
+        -@ $task.cpus \\
+    */
+
+    """
+    echo 'file_in:'
+    echo $file_in
+
+    ashlar \\
+        $file_in
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ashlar: \$(echo \$(ashlar --version 2>&1) | sed 's/^.*ashlar //; s/Using.*\$//' ))
+    END_VERSIONS
+    """
+}

From 54c9029313445cd8f0b04c929ceba656b7741f51 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Tue, 15 Nov 2022 11:31:40 -0500
Subject: [PATCH 017/114] added test image path to test workflow so you can run
 with default test command

---
 tests/modules/nf-core/ashlar/main.nf | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index eb0db7f3b42..7cf39514ac0 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -4,6 +4,8 @@ nextflow.enable.dsl = 2
 
 include { ASHLAR } from '../../../../../modules/modules/nf-core/ashlar/main.nf'
 
+def TEST_IMG = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-06.ome.tiff"
+
 workflow test_ashlar {
 
     println 'running workflow test_ashlar'
@@ -14,8 +16,8 @@ workflow test_ashlar {
     ASHLAR ( input )
     */
 
-    // input_channel = Channel.fromPath( '/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-06.ome.tiff' )
-    input_channel = Channel.fromPath( params.file_in )
+    input_channel = Channel.fromPath( TEST_IMG )
+    //input_channel = Channel.fromPath( params.file_in )
     ASHLAR ( input_channel )
 
     //ASHLAR ( file('/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-06.ome.tiff') )

From cb26c768c997b8ff527523df09a0d5f44e1cdd0c Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Tue, 15 Nov 2022 16:07:43 -0500
Subject: [PATCH 018/114] added ext.args

---
 modules/nf-core/ashlar/main.nf       | 8 +++-----
 tests/modules/nf-core/ashlar/main.nf | 2 +-
 2 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index b50940478ba..65d63dd677b 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -58,7 +58,7 @@ process ASHLAR {
     task.ext.when == null || task.ext.when
 
     script:
-    //def args = task.ext.args ?: ''
+    def args = task.ext.args ?: ''
 
     // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
     //               If the software is unable to output a version number on the command-line then it can be manually specified
@@ -78,11 +78,9 @@ process ASHLAR {
     */
 
     """
-    echo 'file_in:'
-    echo $file_in
-
     ashlar \\
-        $file_in
+        $file_in \\
+        $args
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index 7cf39514ac0..ae0cd2829f3 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -4,7 +4,7 @@ nextflow.enable.dsl = 2
 
 include { ASHLAR } from '../../../../../modules/modules/nf-core/ashlar/main.nf'
 
-def TEST_IMG = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-06.ome.tiff"
+def TEST_IMG = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-0{6,7}.ome.tiff"
 
 workflow test_ashlar {
 

From 828aba3b57a012501a9d8f1e6d6f06088d72824e Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Wed, 16 Nov 2022 13:37:17 -0500
Subject: [PATCH 019/114] added meta map

---
 modules/nf-core/ashlar/main.nf       |  7 ++++---
 modules/nf-core/ashlar/meta.yml      | 12 +++++++++++-
 tests/modules/nf-core/ashlar/main.nf | 10 ++++++++--
 3 files changed, 23 insertions(+), 6 deletions(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 65d63dd677b..ac7490a721f 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -46,7 +46,7 @@ process ASHLAR {
     //               https://github.com/nf-core/modules/blob/master/modules/bwa/index/main.nf
     // TODO nf-core: Where applicable please provide/convert compressed files as input/output
     //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
-    path file_in
+    tuple val(meta), path(file_in)
 
     output:
     // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
@@ -58,7 +58,8 @@ process ASHLAR {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
+    def args_conf = task.ext.args ?: ''
+
 
     // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
     //               If the software is unable to output a version number on the command-line then it can be manually specified
@@ -80,7 +81,7 @@ process ASHLAR {
     """
     ashlar \\
         $file_in \\
-        $args
+        $args_conf
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/ashlar/meta.yml b/modules/nf-core/ashlar/meta.yml
index d0f68c23771..32fa49287b8 100644
--- a/modules/nf-core/ashlar/meta.yml
+++ b/modules/nf-core/ashlar/meta.yml
@@ -15,8 +15,18 @@ tools:
 input:
   #
   ## TODO nf-core: need to add optional and default parameters
+  #- file_in:
+  #    type: file
+  #    description: multidimentional image data in formats from most commercial microscopes
+  #    pattern: "*.ome.tiff"
+
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', test: true ]
   - file_in:
-      type: file
+      type: path
       description: multidimentional image data in formats from most commercial microscopes
       pattern: "*.ome.tiff"
 
diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index ae0cd2829f3..584a1bb4ebc 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -2,9 +2,11 @@
 
 nextflow.enable.dsl = 2
 
+// optional ags go below (if needed): https://nf-co.re/docs/contributing/tutorials/dsl2_modules_tutorial#passing-options-args
 include { ASHLAR } from '../../../../../modules/modules/nf-core/ashlar/main.nf'
 
-def TEST_IMG = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-0{6,7}.ome.tiff"
+//def TEST_IMG = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-0{6,7}.ome.tiff"
+def TEST_IMG = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-06.ome.tiff"
 
 workflow test_ashlar {
 
@@ -18,7 +20,11 @@ workflow test_ashlar {
 
     input_channel = Channel.fromPath( TEST_IMG )
     //input_channel = Channel.fromPath( params.file_in )
-    ASHLAR ( input_channel )
 
     //ASHLAR ( file('/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-06.ome.tiff') )
+
+    input =  [ [ id:'test' ],
+               file(TEST_IMG, checkIfExists: true) ]
+
+    ASHLAR ( input )
 }

From 63e7ebc31e8ba477be4f057f5134d8feb9bd8733 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Wed, 16 Nov 2022 13:58:44 -0500
Subject: [PATCH 020/114] passed test with wildcarded input files

---
 tests/modules/nf-core/ashlar/main.nf | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index 584a1bb4ebc..f086c4e85c7 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -3,10 +3,11 @@
 nextflow.enable.dsl = 2
 
 // optional ags go below (if needed): https://nf-co.re/docs/contributing/tutorials/dsl2_modules_tutorial#passing-options-args
+// TO DO: if they apply to all runs of this workflow they can't they also be in ext.args in nextflow.config?
 include { ASHLAR } from '../../../../../modules/modules/nf-core/ashlar/main.nf'
 
-//def TEST_IMG = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-0{6,7}.ome.tiff"
-def TEST_IMG = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-06.ome.tiff"
+def TEST_IMG = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-0{6,7}.ome.tiff"
+// def TEST_IMG = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-06.ome.tiff"
 
 workflow test_ashlar {
 

From 4970bd3e6358d3b811506be4351349df20404201 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Wed, 16 Nov 2022 14:13:26 -0500
Subject: [PATCH 021/114] added test config file

---
 tests/modules/nf-core/ashlar/nextflow.config | 6 ++++++
 1 file changed, 6 insertions(+)
 create mode 100644 tests/modules/nf-core/ashlar/nextflow.config

diff --git a/tests/modules/nf-core/ashlar/nextflow.config b/tests/modules/nf-core/ashlar/nextflow.config
new file mode 100644
index 00000000000..f4eedcfd783
--- /dev/null
+++ b/tests/modules/nf-core/ashlar/nextflow.config
@@ -0,0 +1,6 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    ext.args = "--flip-x"
+}

From deb9bb5b2c4cca8373cd636108a608816dca6df9 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Wed, 16 Nov 2022 17:20:14 -0500
Subject: [PATCH 022/114] added functionality to handle optional arguments

---
 modules/nf-core/ashlar/functions.nf  | 10 ++++++++++
 modules/nf-core/ashlar/main.nf       | 14 +++++++++++---
 tests/modules/nf-core/ashlar/main.nf |  3 ++-
 3 files changed, 23 insertions(+), 4 deletions(-)
 create mode 100644 modules/nf-core/ashlar/functions.nf

diff --git a/modules/nf-core/ashlar/functions.nf b/modules/nf-core/ashlar/functions.nf
new file mode 100644
index 00000000000..3b25bddeddd
--- /dev/null
+++ b/modules/nf-core/ashlar/functions.nf
@@ -0,0 +1,10 @@
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.publish_by_id   = args.publish_by_id ?: ''
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index ac7490a721f..9a3ba7143f9 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -17,10 +17,15 @@
 
 println 'running main.nf'
 
+include { initOptions } from './functions'
+params.options = [:]
+options = initOptions(params.options)
+
+
 process ASHLAR {
     println 'running process ASHLAR'
 
-    tag '$file_in'
+    tag '$meta.id'
     label 'process_single'
 
     // TODO nf-core: List required Conda package(s).
@@ -59,6 +64,7 @@ process ASHLAR {
 
     script:
     def args_conf = task.ext.args ?: ''
+    def args_opt = options.args ?: ''
 
 
     // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
@@ -74,14 +80,16 @@ process ASHLAR {
     /*
     ashlar \\
         $file_in \\
-        $args \\
+        $args_conf \\
         -@ $task.cpus \\
+        $args_opt
     */
 
     """
     ashlar \\
         $file_in \\
-        $args_conf
+        $args_conf \\
+        $args_opt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index f086c4e85c7..14b09b5c165 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -4,7 +4,8 @@ nextflow.enable.dsl = 2
 
 // optional ags go below (if needed): https://nf-co.re/docs/contributing/tutorials/dsl2_modules_tutorial#passing-options-args
 // TO DO: if they apply to all runs of this workflow they can't they also be in ext.args in nextflow.config?
-include { ASHLAR } from '../../../../../modules/modules/nf-core/ashlar/main.nf'
+include { ASHLAR } from '../../../../../modules/modules/nf-core/ashlar/main.nf' addParams( options: [args: '--flip-mosaic-x'] )
+// include { ASHLAR } from '../../../../../modules/modules/nf-core/ashlar/main.nf'
 
 def TEST_IMG = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-0{6,7}.ome.tiff"
 // def TEST_IMG = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-06.ome.tiff"

From c47d3b6cb10a127ebf7bb408f0d8f8140a9c9e4c Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Thu, 17 Nov 2022 11:49:22 -0500
Subject: [PATCH 023/114] added meta map args

---
 modules/nf-core/ashlar/main.nf       | 4 +++-
 tests/modules/nf-core/ashlar/main.nf | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 9a3ba7143f9..9c0d31ac7e9 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -65,6 +65,7 @@ process ASHLAR {
     script:
     def args_conf = task.ext.args ?: ''
     def args_opt = options.args ?: ''
+    def args_meta = meta.args ?: ''
 
 
     // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
@@ -89,7 +90,8 @@ process ASHLAR {
     ashlar \\
         $file_in \\
         $args_conf \\
-        $args_opt
+        $args_opt \\
+        $args_meta
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index 14b09b5c165..e7260bba0c8 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -25,7 +25,7 @@ workflow test_ashlar {
 
     //ASHLAR ( file('/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-06.ome.tiff') )
 
-    input =  [ [ id:'test' ],
+    input =  [ [ id:'test', args: '--flip-y' ],
                file(TEST_IMG, checkIfExists: true) ]
 
     ASHLAR ( input )

From d555aee1792fb38c359d319dccf6eae502f9c698 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Thu, 17 Nov 2022 12:18:29 -0500
Subject: [PATCH 024/114] supposed to output meta map if you input one

---
 modules/nf-core/ashlar/main.nf | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 9c0d31ac7e9..6fc33418af2 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -56,8 +56,9 @@ process ASHLAR {
     output:
     // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
     // TODO nf-core: List additional required output channels/values here
-    path "*.ome.tif"
-    path "versions.yml"           , emit: versions
+    //path "*.ome.tif"
+    tuple val(meta), path("*.ome.tif"),     emit: ashlar_tif
+    path "versions.yml",                    emit: versions
 
     when:
     task.ext.when == null || task.ext.when

From c8ac4fb412ed6b0b71e8fbfdb044178ef38818b6 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Thu, 17 Nov 2022 15:46:37 -0500
Subject: [PATCH 025/114] clean-up

---
 modules/nf-core/ashlar/main.nf       | 8 +++-----
 tests/modules/nf-core/ashlar/main.nf | 2 ++
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 6fc33418af2..788178d2651 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -21,7 +21,6 @@ include { initOptions } from './functions'
 params.options = [:]
 options = initOptions(params.options)
 
-
 process ASHLAR {
     println 'running process ASHLAR'
 
@@ -33,8 +32,7 @@ process ASHLAR {
     //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
     // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
     // TODO nf-core: need versions for all packages below
-    //conda (params.enable_conda ? "bioconda::ashlar=1.17.0" : null)
-    conda "bioconda::ashlar=1.17.0"
+    conda (params.enable_conda ? "bioconda::ashlar=1.17.0" : null)
 
     /*
     TODO nf-core: how do we referene that we'll
@@ -57,8 +55,8 @@ process ASHLAR {
     // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
     // TODO nf-core: List additional required output channels/values here
     //path "*.ome.tif"
-    tuple val(meta), path("*.ome.tif"),     emit: ashlar_tif
-    path "versions.yml",                    emit: versions
+    tuple val(meta), path("*.ome.tif")  ,   emit: ashlar_tif
+    path "versions.yml"                 ,   emit: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index e7260bba0c8..c94d2598114 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -30,3 +30,5 @@ workflow test_ashlar {
 
     ASHLAR ( input )
 }
+
+// can add additional test workflows below

From 31acde97a66a690078dd0e7e24bd9fcf4adfdba1 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Mon, 21 Nov 2022 16:30:50 -0500
Subject: [PATCH 026/114] changed test input to a channel

---
 tests/modules/nf-core/ashlar/main.nf | 49 +++++++++++++++++++++-------
 1 file changed, 38 insertions(+), 11 deletions(-)

diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index c94d2598114..8afbac5429a 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -9,26 +9,53 @@ include { ASHLAR } from '../../../../../modules/modules/nf-core/ashlar/main.nf'
 
 def TEST_IMG = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-0{6,7}.ome.tiff"
 // def TEST_IMG = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-06.ome.tiff"
+def TEST_SHEET = './input_sheet.csv'
 
 workflow test_ashlar {
 
     println 'running workflow test_ashlar'
 
     /*
-    // TO DO: test with input sample sheet like the following
     input = file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)=
-    ASHLAR ( input )
+    input_channel = Channel.fromList [ input ]
+    ASHLAR ( input_channel )
     */
 
-    input_channel = Channel.fromPath( TEST_IMG )
-    //input_channel = Channel.fromPath( params.file_in )
+    input_list =  [ [ [ id:'test', args: '--flip-y' ],
+               file(TEST_IMG, checkIfExists: true) ] ]
+    input_channel = Channel.fromList(input_list)
 
-    //ASHLAR ( file('/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-06.ome.tiff') )
-
-    input =  [ [ id:'test', args: '--flip-y' ],
-               file(TEST_IMG, checkIfExists: true) ]
-
-    ASHLAR ( input )
+    ASHLAR ( input_channel )
 }
 
-// can add additional test workflows below
+// we can add additional test workflows below
+/*
+include { SAMPLESHEET_CHECK } from '../../../../../modules/modules/nf-core/ashlar/input_check'
+
+workflow test_ashlar_sheet {
+
+    INPUT_CHECK (
+        TEST_SHEET
+    )
+    .input_images
+    .map {
+        meta, fastq ->
+            def meta_clone = meta.clone()
+            meta_clone.id = meta_clone.id.split('_')[0..-2].join('_')
+            [ meta_clone, fastq ]
+    }
+    .groupTuple(by: [0])
+    .branch {
+        meta, fastq ->
+            single  : fastq.size() == 1
+                return [ meta, fastq.flatten() ]
+            multiple: fastq.size() > 1
+                return [ meta, fastq.flatten() ]
+    }
+    .set { ch_fastq }
+
+    // pass meta map of each row of samplesheet to ASHLAR
+
+    ASHLAR ( )
+}
+*/

From 288f590b1ffee63b5e2b0e3664ed1ce94ad3dd46 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Tue, 22 Nov 2022 17:56:37 -0500
Subject: [PATCH 027/114] not running, but close I think

---
 tests/modules/nf-core/ashlar/main.nf | 41 ++++++++++++++--------------
 1 file changed, 21 insertions(+), 20 deletions(-)

diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index 8afbac5429a..d5f7c99d9fd 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -9,7 +9,7 @@ include { ASHLAR } from '../../../../../modules/modules/nf-core/ashlar/main.nf'
 
 def TEST_IMG = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-0{6,7}.ome.tiff"
 // def TEST_IMG = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-06.ome.tiff"
-def TEST_SHEET = './input_sheet.csv'
+def TEST_SHEET = '/home/pollen/github/modules/tests/modules/nf-core/ashlar/input_sheet.csv'
 
 workflow test_ashlar {
 
@@ -29,33 +29,34 @@ workflow test_ashlar {
 }
 
 // we can add additional test workflows below
-/*
-include { SAMPLESHEET_CHECK } from '../../../../../modules/modules/nf-core/ashlar/input_check'
+
+include { INPUT_CHECK } from '../../../../../modules/modules/nf-core/ashlar/input_check.nf'
 
 workflow test_ashlar_sheet {
 
+    /*
     INPUT_CHECK (
         TEST_SHEET
     )
-    .input_images
+    .images
     .map {
-        meta, fastq ->
-            def meta_clone = meta.clone()
-            meta_clone.id = meta_clone.id.split('_')[0..-2].join('_')
-            [ meta_clone, fastq ]
-    }
-    .groupTuple(by: [0])
-    .branch {
-        meta, fastq ->
-            single  : fastq.size() == 1
-                return [ meta, fastq.flatten() ]
-            multiple: fastq.size() > 1
-                return [ meta, fastq.flatten() ]
+        [ [ id:it.id, args: it.args],
+            file(it.file_list, checkIfExists: true) ]
     }
-    .set { ch_fastq }
+    .set { input_maps }
 
-    // pass meta map of each row of samplesheet to ASHLAR
+    ASHLAR ( input_maps )
+    */
+
+    INPUT_CHECK (
+        TEST_SHEET
+    )
+    .images
+    .map {
+        [ [ id:it.id, args: it.args],
+            file(it.file_list, checkIfExists: true) ]
+    }
+    .view { "$it" }
 
-    ASHLAR ( )
 }
-*/
+

From 6843268b81822821ee3028bf4248d0b6bc7a533a Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Tue, 22 Nov 2022 17:58:25 -0500
Subject: [PATCH 028/114] added some missing files

---
 modules/nf-core/ashlar/check_samplesheet.py  | 185 +++++++++++++++++++
 modules/nf-core/ashlar/input_check.nf        |  44 +++++
 modules/nf-core/ashlar/samplesheet_check.nf  |  29 +++
 tests/modules/nf-core/ashlar/input_sheet.csv |   1 +
 4 files changed, 259 insertions(+)
 create mode 100755 modules/nf-core/ashlar/check_samplesheet.py
 create mode 100644 modules/nf-core/ashlar/input_check.nf
 create mode 100644 modules/nf-core/ashlar/samplesheet_check.nf
 create mode 100644 tests/modules/nf-core/ashlar/input_sheet.csv

diff --git a/modules/nf-core/ashlar/check_samplesheet.py b/modules/nf-core/ashlar/check_samplesheet.py
new file mode 100755
index 00000000000..1902d2d2995
--- /dev/null
+++ b/modules/nf-core/ashlar/check_samplesheet.py
@@ -0,0 +1,185 @@
+#!/home/pollen/anaconda3/bin/python3
+
+import os
+import sys
+import errno
+import argparse
+
+
+def parse_args(args=None):
+    Description = "Reformat nf-core/rnaseq samplesheet file and check its contents."
+    Epilog = "Example usage: python check_samplesheet.py <FILE_IN> <FILE_OUT>"
+
+    parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
+    parser.add_argument("FILE_IN", help="Input samplesheet file.")
+    parser.add_argument("FILE_OUT", help="Output file.")
+    return parser.parse_args(args)
+
+
+def make_dir(path):
+    if len(path) > 0:
+        try:
+            os.makedirs(path)
+        except OSError as exception:
+            if exception.errno != errno.EEXIST:
+                raise exception
+
+
+def print_error(error, context="Line", context_str=""):
+    error_str = f"ERROR: Please check samplesheet -> {error}"
+    if context != "" and context_str != "":
+        error_str = f"ERROR: Please check samplesheet -> {error}\n{context.strip()}: '{context_str.strip()}'"
+    print(error_str)
+    sys.exit(1)
+
+
+def check_samplesheet(file_in, file_out):
+    """
+    This function checks that the samplesheet follows the following structure:
+    sample,input_file_list,optional_args
+    https://github.com/nf-core/test-datasets/blob/rnaseq/samplesheet/v3.1/samplesheet_test.csv
+    """
+
+    """
+    sample_mapping_dict = {}
+    with open(file_in, "r", encoding='utf-8-sig') as fin:
+
+        ## Check header
+        MIN_COLS = 3
+        HEADER = ["sample", "input_file_list", "optional_args"]
+        header = [x.strip('"') for x in fin.readline().strip().split(",")]
+        if header[: len(HEADER)] != HEADER:
+            print(
+                f"ERROR: Please check samplesheet header -> {','.join(header)} != {','.join(HEADER)}"
+            )
+            sys.exit(1)
+
+        ## Check sample entries
+        for line in fin:
+            if line.strip():
+                lspl = [x.strip().strip('"') for x in line.strip().split(",")]
+
+                ## Check valid number of columns per row
+                if len(lspl) < len(HEADER):
+                    print_error(
+                        f"Invalid number of columns (minimum = {len(HEADER)})!",
+                        "Line",
+                        line,
+                    )
+
+                num_cols = len([x for x in lspl if x])
+                if num_cols < MIN_COLS:
+                    print_error(
+                        f"Invalid number of populated columns (minimum = {MIN_COLS})!",
+                        "Line",
+                        line,
+                    )
+
+                ## Check sample name entries
+                sample, fastq_1, fastq_2, strandedness = lspl[: len(HEADER)]
+                if sample.find(" ") != -1:
+                    print(
+                        f"WARNING: Spaces have been replaced by underscores for sample: {sample}"
+                    )
+                    sample = sample.replace(" ", "_")
+                if not sample:
+                    print_error("Sample entry has not been specified!", "Line", line)
+
+                ## Check FastQ file extension
+                for fastq in [fastq_1, fastq_2]:
+                    if fastq:
+                        if fastq.find(" ") != -1:
+                            print_error("FastQ file contains spaces!", "Line", line)
+                        if not fastq.endswith(".fastq.gz") and not fastq.endswith(".fq.gz"):
+                            print_error(
+                                "FastQ file does not have extension '.fastq.gz' or '.fq.gz'!",
+                                "Line",
+                                line,
+                            )
+
+                ## Check strandedness
+                strandednesses = ["unstranded", "forward", "reverse"]
+                if strandedness:
+                    if strandedness not in strandednesses:
+                        print_error(
+                            f"Strandedness must be one of '{', '.join(strandednesses)}'!",
+                            "Line",
+                            line,
+                        )
+                else:
+                    print_error(
+                        f"Strandedness has not been specified! Must be one of {', '.join(strandednesses)}.",
+                        "Line",
+                        line,
+                    )
+
+                ## Auto-detect paired-end/single-end
+                sample_info = []  ## [single_end, fastq_1, fastq_2, strandedness]
+                if sample and fastq_1 and fastq_2:  ## Paired-end short reads
+                    sample_info = ["0", fastq_1, fastq_2, strandedness]
+                elif sample and fastq_1 and not fastq_2:  ## Single-end short reads
+                    sample_info = ["1", fastq_1, fastq_2, strandedness]
+                else:
+                    print_error("Invalid combination of columns provided!", "Line", line)
+
+                ## Create sample mapping dictionary = {sample: [[ single_end, fastq_1, fastq_2, strandedness ]]}
+                if sample not in sample_mapping_dict:
+                    sample_mapping_dict[sample] = [sample_info]
+                else:
+                    if sample_info in sample_mapping_dict[sample]:
+                        print_error("Samplesheet contains duplicate rows!", "Line", line)
+                    else:
+                        sample_mapping_dict[sample].append(sample_info)
+
+    ## Write validated samplesheet with appropriate columns
+    if len(sample_mapping_dict) > 0:
+        out_dir = os.path.dirname(file_out)
+        make_dir(out_dir)
+        with open(file_out, "w") as fout:
+            fout.write(
+                ",".join(["sample", "single_end", "fastq_1", "fastq_2", "strandedness"])
+                + "\n"
+            )
+            for sample in sorted(sample_mapping_dict.keys()):
+
+                ## Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end
+                if not all(
+                    x[0] == sample_mapping_dict[sample][0][0]
+                    for x in sample_mapping_dict[sample]
+                ):
+                    print_error(
+                        f"Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end!",
+                        "Sample",
+                        sample,
+                    )
+
+                ## Check that multiple runs of the same sample are of the same strandedness
+                if not all(
+                    x[-1] == sample_mapping_dict[sample][0][-1]
+                    for x in sample_mapping_dict[sample]
+                ):
+                    print_error(
+                        f"Multiple runs of a sample must have the same strandedness!",
+                        "Sample",
+                        sample,
+                    )
+
+                for idx, val in enumerate(sample_mapping_dict[sample]):
+                    fout.write(",".join([f"{sample}_T{idx+1}"] + val) + "\n")
+    else:
+        print_error(f"No entries to process!", "Samplesheet: {file_in}")
+    """
+
+    with open(file_in, "r", encoding='utf-8-sig') as fin:
+        with open(file_out, "w") as fout:
+            for line in fin:
+                fout.write(line)
+
+
+def main(args=None):
+    args = parse_args(args)
+    check_samplesheet(args.FILE_IN, args.FILE_OUT)
+
+
+if __name__ == "__main__":
+    sys.exit(main())
diff --git a/modules/nf-core/ashlar/input_check.nf b/modules/nf-core/ashlar/input_check.nf
new file mode 100644
index 00000000000..0f5f76ccea5
--- /dev/null
+++ b/modules/nf-core/ashlar/input_check.nf
@@ -0,0 +1,44 @@
+include { SAMPLESHEET_CHECK } from './samplesheet_check'
+
+workflow INPUT_CHECK {
+
+    take:
+    samplesheet  // file: ./input_sheet.csv
+
+    main:
+    SAMPLESHEET_CHECK ( samplesheet )
+        .csv
+        .splitCsv (header:true, sep:',')
+        .map { create_image_channel(it) }
+        .set { images }
+
+    emit:
+    images                                     // channel: [ val(meta), path(image) ]
+    versions = SAMPLESHEET_CHECK.out.versions  // channel: [ versions.yml ]
+}
+
+def create_image_channel(LinkedHashMap row) {
+    // create meta map
+    /*
+    def meta = [:]
+    meta.id           = row.sample
+    meta.single_end   = row.single_end.toBoolean()
+    meta.strandedness = row.strandedness
+
+    // add path(s) of the fastq file(s) to the meta map
+    def fastq_meta = []
+    if (!file(row.fastq_1).exists()) {
+        exit 1, "ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!\n${row.fastq_1}"
+    }
+    if (meta.single_end) {
+        fastq_meta = [ meta, [ file(row.fastq_1) ] ]
+    } else {
+        if (!file(row.fastq_2).exists()) {
+            exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}"
+        }
+        fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
+    }
+    return fastq_meta
+    */
+    return row
+}
diff --git a/modules/nf-core/ashlar/samplesheet_check.nf b/modules/nf-core/ashlar/samplesheet_check.nf
new file mode 100644
index 00000000000..e709486ab82
--- /dev/null
+++ b/modules/nf-core/ashlar/samplesheet_check.nf
@@ -0,0 +1,29 @@
+process SAMPLESHEET_CHECK {
+    tag "$samplesheet"
+
+    conda (params.enable_conda ? "conda-forge::python=3.9.5" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/python:3.9--1' :
+        'quay.io/biocontainers/python:3.9--1' }"
+
+    input:
+    path samplesheet
+
+    output:
+    path '*.csv'       , emit: csv
+    path "versions.yml", emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script: // This script is bundled with the pipeline, in nf-core/rnaseq/bin/
+    """
+    /home/pollen/github/modules/modules/nf-core/ashlar/check_samplesheet.py \\
+        $samplesheet \\
+        samplesheet.valid.csv
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python --version | sed 's/Python //g')
+    END_VERSIONS
+    """
+}
diff --git a/tests/modules/nf-core/ashlar/input_sheet.csv b/tests/modules/nf-core/ashlar/input_sheet.csv
new file mode 100644
index 00000000000..e525aec6bc3
--- /dev/null
+++ b/tests/modules/nf-core/ashlar/input_sheet.csv
@@ -0,0 +1 @@
+test_1,/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-06.ome.tiff,'--flip-mosaic-x'

From 69a807c16d26eda6da197bfeb2ebfb60dff68715 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Mon, 28 Nov 2022 17:21:00 -0500
Subject: [PATCH 029/114] basic samplesheet working

---
 modules/nf-core/ashlar/input_check.nf        |  3 +++
 tests/modules/nf-core/ashlar/input_sheet.csv |  3 ++-
 tests/modules/nf-core/ashlar/main.nf         | 25 ++++----------------
 3 files changed, 9 insertions(+), 22 deletions(-)

diff --git a/modules/nf-core/ashlar/input_check.nf b/modules/nf-core/ashlar/input_check.nf
index 0f5f76ccea5..a434135b855 100644
--- a/modules/nf-core/ashlar/input_check.nf
+++ b/modules/nf-core/ashlar/input_check.nf
@@ -2,6 +2,8 @@ include { SAMPLESHEET_CHECK } from './samplesheet_check'
 
 workflow INPUT_CHECK {
 
+    println "running INPUT_CHECK..."
+
     take:
     samplesheet  // file: ./input_sheet.csv
 
@@ -10,6 +12,7 @@ workflow INPUT_CHECK {
         .csv
         .splitCsv (header:true, sep:',')
         .map { create_image_channel(it) }
+        .view()
         .set { images }
 
     emit:
diff --git a/tests/modules/nf-core/ashlar/input_sheet.csv b/tests/modules/nf-core/ashlar/input_sheet.csv
index e525aec6bc3..4cf6df6074a 100644
--- a/tests/modules/nf-core/ashlar/input_sheet.csv
+++ b/tests/modules/nf-core/ashlar/input_sheet.csv
@@ -1 +1,2 @@
-test_1,/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-06.ome.tiff,'--flip-mosaic-x'
+sample,file_list,args
+test1,/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-06.ome.tiff,'--flip-mosaic-x'
diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index d5f7c99d9fd..74f58706cda 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -13,14 +13,6 @@ def TEST_SHEET = '/home/pollen/github/modules/tests/modules/nf-core/ashlar/input
 
 workflow test_ashlar {
 
-    println 'running workflow test_ashlar'
-
-    /*
-    input = file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)=
-    input_channel = Channel.fromList [ input ]
-    ASHLAR ( input_channel )
-    */
-
     input_list =  [ [ [ id:'test', args: '--flip-y' ],
                file(TEST_IMG, checkIfExists: true) ] ]
     input_channel = Channel.fromList(input_list)
@@ -28,15 +20,17 @@ workflow test_ashlar {
     ASHLAR ( input_channel )
 }
 
+
 // we can add additional test workflows below
 
 include { INPUT_CHECK } from '../../../../../modules/modules/nf-core/ashlar/input_check.nf'
 
 workflow test_ashlar_sheet {
 
-    /*
+    ch_input = file(TEST_SHEET)
+
     INPUT_CHECK (
-        TEST_SHEET
+        ch_input
     )
     .images
     .map {
@@ -46,17 +40,6 @@ workflow test_ashlar_sheet {
     .set { input_maps }
 
     ASHLAR ( input_maps )
-    */
-
-    INPUT_CHECK (
-        TEST_SHEET
-    )
-    .images
-    .map {
-        [ [ id:it.id, args: it.args],
-            file(it.file_list, checkIfExists: true) ]
-    }
-    .view { "$it" }
 
 }
 

From eaa39c37bf6b686dba78a4756de69eb4881b3276 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Tue, 29 Nov 2022 12:36:47 -0500
Subject: [PATCH 030/114] clean-up post testing

---
 tests/modules/nf-core/ashlar/input_sheet.csv | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/modules/nf-core/ashlar/input_sheet.csv b/tests/modules/nf-core/ashlar/input_sheet.csv
index 4cf6df6074a..535790e29e4 100644
--- a/tests/modules/nf-core/ashlar/input_sheet.csv
+++ b/tests/modules/nf-core/ashlar/input_sheet.csv
@@ -1,2 +1,3 @@
 sample,file_list,args
-test1,/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-06.ome.tiff,'--flip-mosaic-x'
+test_1,/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-07.ome.tiff,'--flip-mosaic-x'
+test_2,/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-08.ome.tiff,'--flip-mosaic-x'

From b57595a178c0654dfbed0e1059c4491aa9dbb70e Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Wed, 30 Nov 2022 13:56:48 -0500
Subject: [PATCH 031/114] enabled multiple input images

---
 modules/nf-core/ashlar/main.nf               |  3 ++-
 tests/modules/nf-core/ashlar/input_sheet.csv |  2 +-
 tests/modules/nf-core/ashlar/main.nf         | 21 +++++++++++++++++++-
 3 files changed, 23 insertions(+), 3 deletions(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 788178d2651..5590f58ca2d 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -49,7 +49,8 @@ process ASHLAR {
     //               https://github.com/nf-core/modules/blob/master/modules/bwa/index/main.nf
     // TODO nf-core: Where applicable please provide/convert compressed files as input/output
     //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
-    tuple val(meta), path(file_in)
+    //tuple val(meta), path(file_in)
+    tuple val(meta), val(file_in)
 
     output:
     // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
diff --git a/tests/modules/nf-core/ashlar/input_sheet.csv b/tests/modules/nf-core/ashlar/input_sheet.csv
index 535790e29e4..43b4c1d4444 100644
--- a/tests/modules/nf-core/ashlar/input_sheet.csv
+++ b/tests/modules/nf-core/ashlar/input_sheet.csv
@@ -1,3 +1,3 @@
 sample,file_list,args
-test_1,/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-07.ome.tiff,'--flip-mosaic-x'
+test_1,/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-06.ome.tiff /home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-07.ome.tiff,'--flip-mosaic-x'
 test_2,/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-08.ome.tiff,'--flip-mosaic-x'
diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index 74f58706cda..e20507d0069 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -8,14 +8,21 @@ include { ASHLAR } from '../../../../../modules/modules/nf-core/ashlar/main.nf'
 // include { ASHLAR } from '../../../../../modules/modules/nf-core/ashlar/main.nf'
 
 def TEST_IMG = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-0{6,7}.ome.tiff"
-// def TEST_IMG = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-06.ome.tiff"
+def TEST_IMG_1 = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-06.ome.tiff"
+def TEST_IMG_2 = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-07.ome.tiff"
 def TEST_SHEET = '/home/pollen/github/modules/tests/modules/nf-core/ashlar/input_sheet.csv'
 
 workflow test_ashlar {
 
+    /* works
     input_list =  [ [ [ id:'test', args: '--flip-y' ],
                file(TEST_IMG, checkIfExists: true) ] ]
     input_channel = Channel.fromList(input_list)
+    */
+
+    input_list =  [ [ [ id:'test', args: '--flip-y' ],
+               "${TEST_IMG_1} ${TEST_IMG_2}" ] ]
+    input_channel = Channel.fromList(input_list)
 
     ASHLAR ( input_channel )
 }
@@ -29,6 +36,7 @@ workflow test_ashlar_sheet {
 
     ch_input = file(TEST_SHEET)
 
+    /* works
     INPUT_CHECK (
         ch_input
     )
@@ -38,6 +46,17 @@ workflow test_ashlar_sheet {
             file(it.file_list, checkIfExists: true) ]
     }
     .set { input_maps }
+    */
+
+    INPUT_CHECK (
+        ch_input
+    )
+    .images
+    .map {
+        [ [ id:it.id, args: it.args],
+            it.file_list ]
+    }
+    .set { input_maps }
 
     ASHLAR ( input_maps )
 

From 125281fb51a0ac8a475921562491a7430057b337 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Wed, 30 Nov 2022 15:38:50 -0500
Subject: [PATCH 032/114] bug fix: sheet meta arg not an it var

---
 modules/nf-core/ashlar/main.nf       | 2 ++
 tests/modules/nf-core/ashlar/main.nf | 2 +-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 5590f58ca2d..048564b055b 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -63,6 +63,8 @@ process ASHLAR {
     task.ext.when == null || task.ext.when
 
     script:
+    println meta.args
+
     def args_conf = task.ext.args ?: ''
     def args_opt = options.args ?: ''
     def args_meta = meta.args ?: ''
diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index e20507d0069..e2501434aab 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -53,7 +53,7 @@ workflow test_ashlar_sheet {
     )
     .images
     .map {
-        [ [ id:it.id, args: it.args],
+        [ [ id:it.id, args: '--flip-y' ],
             it.file_list ]
     }
     .set { input_maps }

From 9f98637761e81adc95262a011f14e366b056d921 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Wed, 30 Nov 2022 16:32:04 -0500
Subject: [PATCH 033/114] clean-up

---
 tests/modules/nf-core/ashlar/main.nf | 19 -------------------
 1 file changed, 19 deletions(-)

diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index e2501434aab..2fa5c93a406 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -14,12 +14,6 @@ def TEST_SHEET = '/home/pollen/github/modules/tests/modules/nf-core/ashlar/input
 
 workflow test_ashlar {
 
-    /* works
-    input_list =  [ [ [ id:'test', args: '--flip-y' ],
-               file(TEST_IMG, checkIfExists: true) ] ]
-    input_channel = Channel.fromList(input_list)
-    */
-
     input_list =  [ [ [ id:'test', args: '--flip-y' ],
                "${TEST_IMG_1} ${TEST_IMG_2}" ] ]
     input_channel = Channel.fromList(input_list)
@@ -36,18 +30,6 @@ workflow test_ashlar_sheet {
 
     ch_input = file(TEST_SHEET)
 
-    /* works
-    INPUT_CHECK (
-        ch_input
-    )
-    .images
-    .map {
-        [ [ id:it.id, args: it.args],
-            file(it.file_list, checkIfExists: true) ]
-    }
-    .set { input_maps }
-    */
-
     INPUT_CHECK (
         ch_input
     )
@@ -61,4 +43,3 @@ workflow test_ashlar_sheet {
     ASHLAR ( input_maps )
 
 }
-

From 9c17dff4aca0d817f9b82499a33ef98fe6e973fd Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Thu, 1 Dec 2022 17:20:54 -0500
Subject: [PATCH 034/114] added samplesheet validation

---
 modules/nf-core/ashlar/check_samplesheet.py | 89 ++++++---------------
 modules/nf-core/ashlar/main.nf              |  6 +-
 2 files changed, 29 insertions(+), 66 deletions(-)

diff --git a/modules/nf-core/ashlar/check_samplesheet.py b/modules/nf-core/ashlar/check_samplesheet.py
index 1902d2d2995..561d2e40f2a 100755
--- a/modules/nf-core/ashlar/check_samplesheet.py
+++ b/modules/nf-core/ashlar/check_samplesheet.py
@@ -36,17 +36,15 @@ def print_error(error, context="Line", context_str=""):
 def check_samplesheet(file_in, file_out):
     """
     This function checks that the samplesheet follows the following structure:
-    sample,input_file_list,optional_args
-    https://github.com/nf-core/test-datasets/blob/rnaseq/samplesheet/v3.1/samplesheet_test.csv
+    sample,file_list,args
     """
 
-    """
     sample_mapping_dict = {}
     with open(file_in, "r", encoding='utf-8-sig') as fin:
 
         ## Check header
         MIN_COLS = 3
-        HEADER = ["sample", "input_file_list", "optional_args"]
+        HEADER = ["sample", "file_list", "args"]
         header = [x.strip('"') for x in fin.readline().strip().split(",")]
         if header[: len(HEADER)] != HEADER:
             print(
@@ -76,7 +74,7 @@ def check_samplesheet(file_in, file_out):
                     )
 
                 ## Check sample name entries
-                sample, fastq_1, fastq_2, strandedness = lspl[: len(HEADER)]
+                sample, file_list, args = lspl[: len(HEADER)]
                 if sample.find(" ") != -1:
                     print(
                         f"WARNING: Spaces have been replaced by underscores for sample: {sample}"
@@ -85,44 +83,29 @@ def check_samplesheet(file_in, file_out):
                 if not sample:
                     print_error("Sample entry has not been specified!", "Line", line)
 
-                ## Check FastQ file extension
-                for fastq in [fastq_1, fastq_2]:
-                    if fastq:
-                        if fastq.find(" ") != -1:
-                            print_error("FastQ file contains spaces!", "Line", line)
-                        if not fastq.endswith(".fastq.gz") and not fastq.endswith(".fq.gz"):
+                ## Check input files
+                if file_list:
+                    print('file_list: {}'.format(file_list))
+                    if file_list.find(" ") != -1:
+                        file_list_list = file_list.split(' ')
+                    else:
+                        file_list_list = [file_list]
+                    print(file_list_list)
+                    for input_file in file_list_list:
+                        print('current input file: {}'.format(input_file))
+                        if not os.path.exists(input_file):
+                            print_error("Input file does not exist!", "Line", line)
+                        if not input_file.endswith(".tiff"):
                             print_error(
-                                "FastQ file does not have extension '.fastq.gz' or '.fq.gz'!",
-                                "Line",
-                                line,
-                            )
-
-                ## Check strandedness
-                strandednesses = ["unstranded", "forward", "reverse"]
-                if strandedness:
-                    if strandedness not in strandednesses:
-                        print_error(
-                            f"Strandedness must be one of '{', '.join(strandednesses)}'!",
-                            "Line",
-                            line,
-                        )
+                                "Input image file must have extension '.tiff' or '.ome.tiff'!",
+                                "Line", line)
                 else:
-                    print_error(
-                        f"Strandedness has not been specified! Must be one of {', '.join(strandednesses)}.",
-                        "Line",
-                        line,
-                    )
+                    print_error("Each run must include at least one input image!", "Line", line)
 
-                ## Auto-detect paired-end/single-end
-                sample_info = []  ## [single_end, fastq_1, fastq_2, strandedness]
-                if sample and fastq_1 and fastq_2:  ## Paired-end short reads
-                    sample_info = ["0", fastq_1, fastq_2, strandedness]
-                elif sample and fastq_1 and not fastq_2:  ## Single-end short reads
-                    sample_info = ["1", fastq_1, fastq_2, strandedness]
-                else:
-                    print_error("Invalid combination of columns provided!", "Line", line)
+                ## Check optional arguments
+                # TO DO: ashlar will error on bad arguments, so do we need to do any checking here?
 
-                ## Create sample mapping dictionary = {sample: [[ single_end, fastq_1, fastq_2, strandedness ]]}
+                sample_info = [file_list, args]
                 if sample not in sample_mapping_dict:
                     sample_mapping_dict[sample] = [sample_info]
                 else:
@@ -137,44 +120,22 @@ def check_samplesheet(file_in, file_out):
         make_dir(out_dir)
         with open(file_out, "w") as fout:
             fout.write(
-                ",".join(["sample", "single_end", "fastq_1", "fastq_2", "strandedness"])
+                ",".join(["sample", "file_list", "args"])
                 + "\n"
             )
             for sample in sorted(sample_mapping_dict.keys()):
 
-                ## Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end
-                if not all(
-                    x[0] == sample_mapping_dict[sample][0][0]
-                    for x in sample_mapping_dict[sample]
-                ):
-                    print_error(
-                        f"Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end!",
-                        "Sample",
-                        sample,
-                    )
-
-                ## Check that multiple runs of the same sample are of the same strandedness
-                if not all(
-                    x[-1] == sample_mapping_dict[sample][0][-1]
-                    for x in sample_mapping_dict[sample]
-                ):
-                    print_error(
-                        f"Multiple runs of a sample must have the same strandedness!",
-                        "Sample",
-                        sample,
-                    )
-
                 for idx, val in enumerate(sample_mapping_dict[sample]):
                     fout.write(",".join([f"{sample}_T{idx+1}"] + val) + "\n")
     else:
         print_error(f"No entries to process!", "Samplesheet: {file_in}")
-    """
 
+    '''
     with open(file_in, "r", encoding='utf-8-sig') as fin:
         with open(file_out, "w") as fout:
             for line in fin:
                 fout.write(line)
-
+    '''
 
 def main(args=None):
     args = parse_args(args)
diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 048564b055b..cc990b1b52a 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -24,6 +24,9 @@ options = initOptions(params.options)
 process ASHLAR {
     println 'running process ASHLAR'
 
+    // publishDir "/tmp/tmpOUTPUT/ashlar_results", pattern: "${meta.id}.ome.tif"
+    // publishDir = [ path: { "${params.outdir}/${meta.id}/" } ]
+
     tag '$meta.id'
     label 'process_single'
 
@@ -57,14 +60,13 @@ process ASHLAR {
     // TODO nf-core: List additional required output channels/values here
     //path "*.ome.tif"
     tuple val(meta), path("*.ome.tif")  ,   emit: ashlar_tif
+    // tuple val(meta), path("${meta.id}.ome.tif")  ,   emit: ashlar_tif
     path "versions.yml"                 ,   emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    println meta.args
-
     def args_conf = task.ext.args ?: ''
     def args_opt = options.args ?: ''
     def args_meta = meta.args ?: ''

From 1f457910468c18936365cfde67d8acae135fffb7 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Sat, 3 Dec 2022 00:49:57 -0500
Subject: [PATCH 035/114] samplesheet output to subdirs with sample name; needs
 clean-up

---
 modules/nf-core/ashlar/check_samplesheet.py | 3 ++-
 modules/nf-core/ashlar/main.nf              | 4 +++-
 tests/modules/nf-core/ashlar/main.nf        | 5 ++---
 3 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/modules/nf-core/ashlar/check_samplesheet.py b/modules/nf-core/ashlar/check_samplesheet.py
index 561d2e40f2a..a7e7b865760 100755
--- a/modules/nf-core/ashlar/check_samplesheet.py
+++ b/modules/nf-core/ashlar/check_samplesheet.py
@@ -126,7 +126,8 @@ def check_samplesheet(file_in, file_out):
             for sample in sorted(sample_mapping_dict.keys()):
 
                 for idx, val in enumerate(sample_mapping_dict[sample]):
-                    fout.write(",".join([f"{sample}_T{idx+1}"] + val) + "\n")
+                    fout.write(",".join([f"{sample}"] + val) + "\n")
+#                    fout.write(",".join([f"{sample}_T{idx+1}"] + val) + "\n")
     else:
         print_error(f"No entries to process!", "Samplesheet: {file_in}")
 
diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index cc990b1b52a..d1500914169 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -25,7 +25,7 @@ process ASHLAR {
     println 'running process ASHLAR'
 
     // publishDir "/tmp/tmpOUTPUT/ashlar_results", pattern: "${meta.id}.ome.tif"
-    // publishDir = [ path: { "${params.outdir}/${meta.id}/" } ]
+    publishDir = [ path: { "${params.outdir}/foo/${meta.id}/" } ]
 
     tag '$meta.id'
     label 'process_single'
@@ -71,6 +71,8 @@ process ASHLAR {
     def args_opt = options.args ?: ''
     def args_meta = meta.args ?: ''
 
+    debug_file = new File('/tmp/tmp_debug/log.txt')
+    debug_file.write "${meta.id}  ${meta.sample}  ${meta.args}"
 
     // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
     //               If the software is unable to output a version number on the command-line then it can be manually specified
diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index 2fa5c93a406..f1d3f01c0cf 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -21,7 +21,6 @@ workflow test_ashlar {
     ASHLAR ( input_channel )
 }
 
-
 // we can add additional test workflows below
 
 include { INPUT_CHECK } from '../../../../../modules/modules/nf-core/ashlar/input_check.nf'
@@ -35,8 +34,8 @@ workflow test_ashlar_sheet {
     )
     .images
     .map {
-        [ [ id:it.id, args: '--flip-y' ],
-            it.file_list ]
+        it -> [ [ id: it.sample, args: '--flip-y' ],
+                it.file_list ]
     }
     .set { input_maps }
 

From 9bc2269b144b9a8ced32a40ec0230d22ad098d25 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Fri, 9 Dec 2022 12:28:47 -0500
Subject: [PATCH 036/114] cleaned up meta.yml and passed test

---
 modules/nf-core/ashlar/main.nf  |  3 ++-
 modules/nf-core/ashlar/meta.yml | 26 +++++++++++---------------
 2 files changed, 13 insertions(+), 16 deletions(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index d1500914169..e7da76135be 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -71,8 +71,10 @@ process ASHLAR {
     def args_opt = options.args ?: ''
     def args_meta = meta.args ?: ''
 
+    /*
     debug_file = new File('/tmp/tmp_debug/log.txt')
     debug_file.write "${meta.id}  ${meta.sample}  ${meta.args}"
+    */
 
     // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
     //               If the software is unable to output a version number on the command-line then it can be manually specified
@@ -88,7 +90,6 @@ process ASHLAR {
     ashlar \\
         $file_in \\
         $args_conf \\
-        -@ $task.cpus \\
         $args_opt
     */
 
diff --git a/modules/nf-core/ashlar/meta.yml b/modules/nf-core/ashlar/meta.yml
index 32fa49287b8..58fa63c934c 100644
--- a/modules/nf-core/ashlar/meta.yml
+++ b/modules/nf-core/ashlar/meta.yml
@@ -8,23 +8,16 @@ tools:
       description: "Alignment by Simultaneous Harmonization of Layer/Adjacency Registration"
       homepage: "https://labsyspharm.github.io/ashlar/"
       documentation: "https://labsyspharm.github.io/ashlar/"
-      tool_dev_url: "None"
       doi: "10.1101/2021.04.20.440625"
       licence: "['MIT']"
 
 input:
   #
-  ## TODO nf-core: need to add optional and default parameters
-  #- file_in:
-  #    type: file
-  #    description: multidimentional image data in formats from most commercial microscopes
-  #    pattern: "*.ome.tiff"
-
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
-        e.g. [ id:'test', test: true ]
+        e.g. [ id:'test', : args: '--flip-x' ]
   - file_in:
       type: path
       description: multidimentional image data in formats from most commercial microscopes
@@ -32,17 +25,20 @@ input:
 
 output:
   #
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', : args: '--flip-x' ]
+  - file_out:
+      type: file
+      description: pyramidal OME-TIFF
+      pattern: "*.tif"
   - versions:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-  ## TODO nf-core: This just handles one output option.  We also have to handle the case
-  ##               where the user requests a series of single-channel plain TIFF files
-  ##               by setting the output filename to *.tif
-  - file_out:
-      type: file
-      description: pyramidal OME-TIFF
-      pattern: "*.ome.tif"
 
 authors:
   - "@RobJY"
+  - "@jmuhlich"

From f6bedd07f13842a79117a923b8e2eb5a4a0943f8 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Fri, 9 Dec 2022 15:48:09 -0500
Subject: [PATCH 037/114] clean-up; passed tests

---
 modules/nf-core/ashlar/main.nf       | 72 ++--------------------------
 tests/modules/nf-core/ashlar/main.nf |  6 +--
 2 files changed, 5 insertions(+), 73 deletions(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index e7da76135be..1abb41cc344 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -1,66 +1,24 @@
-// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
-//               https://github.com/nf-core/modules/tree/master/modules
-//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
-//               https://nf-co.re/join
-// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
-//               All other parameters MUST be provided using the "task.ext" directive, see here:
-//               https://www.nextflow.io/docs/latest/process.html#ext
-//               where "task.ext" is a string.
-//               Any parameters that need to be evaluated in the context of a particular sample
-//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
-// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
-//               unless there is a run-time, storage advantage in implementing in this way
-//               e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
-//                 bwa mem | samtools view -B -T ref.fasta
-// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
-//               list (`[]`) instead of a file can be used to work around this issue.
-
-println 'running main.nf'
-
 include { initOptions } from './functions'
 params.options = [:]
 options = initOptions(params.options)
 
 process ASHLAR {
-    println 'running process ASHLAR'
-
-    // publishDir "/tmp/tmpOUTPUT/ashlar_results", pattern: "${meta.id}.ome.tif"
-    publishDir = [ path: { "${params.outdir}/foo/${meta.id}/" } ]
+    publishDir = [ path: { "${params.outdir}/${meta.id}/" } ]
 
     tag '$meta.id'
     label 'process_single'
 
-    // TODO nf-core: List required Conda package(s).
-    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
-    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
-    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
-    // TODO nf-core: need versions for all packages below
     conda (params.enable_conda ? "bioconda::ashlar=1.17.0" : null)
-
-    /*
-    TODO nf-core: how do we referene that we'll
+    // TODO nf-core: need to have this added
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE':
-        'quay.io/biocontainers/YOUR-TOOL-HERE' }"
-    */
-    //container "/home/pollen/github/modules/modules/nf-core/ashlar/ashlar.img"
+        'https://depot.galaxyproject.org/singularity/ashlar':
+        'quay.io/biocontainers/ashlar' }"
 
     input:
-    // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
-    //               MUST be provided as an input via a Groovy Map called "meta".
-    //               This information may not be required in some instances e.g. indexing reference genome files:
-    //               https://github.com/nf-core/modules/blob/master/modules/bwa/index/main.nf
-    // TODO nf-core: Where applicable please provide/convert compressed files as input/output
-    //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
-    //tuple val(meta), path(file_in)
     tuple val(meta), val(file_in)
 
     output:
-    // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
-    // TODO nf-core: List additional required output channels/values here
-    //path "*.ome.tif"
     tuple val(meta), path("*.ome.tif")  ,   emit: ashlar_tif
-    // tuple val(meta), path("${meta.id}.ome.tif")  ,   emit: ashlar_tif
     path "versions.yml"                 ,   emit: versions
 
     when:
@@ -71,28 +29,6 @@ process ASHLAR {
     def args_opt = options.args ?: ''
     def args_meta = meta.args ?: ''
 
-    /*
-    debug_file = new File('/tmp/tmp_debug/log.txt')
-    debug_file.write "${meta.id}  ${meta.sample}  ${meta.args}"
-    */
-
-    // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
-    //               If the software is unable to output a version number on the command-line then it can be manually specified
-    //               e.g. https://github.com/nf-core/modules/blob/master/modules/homer/annotatepeaks/main.nf
-    //               Each software used MUST provide the software name and version number in the YAML version file (versions.yml)
-    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
-    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
-    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
-    // TODO nf-core: Please replace the example samtools command below with your module's command
-    // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
-
-    /*
-    ashlar \\
-        $file_in \\
-        $args_conf \\
-        $args_opt
-    */
-
     """
     ashlar \\
         $file_in \\
diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index f1d3f01c0cf..1a83e3380a7 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -2,10 +2,8 @@
 
 nextflow.enable.dsl = 2
 
-// optional ags go below (if needed): https://nf-co.re/docs/contributing/tutorials/dsl2_modules_tutorial#passing-options-args
-// TO DO: if they apply to all runs of this workflow they can't they also be in ext.args in nextflow.config?
-include { ASHLAR } from '../../../../../modules/modules/nf-core/ashlar/main.nf' addParams( options: [args: '--flip-mosaic-x'] )
 // include { ASHLAR } from '../../../../../modules/modules/nf-core/ashlar/main.nf'
+include { ASHLAR } from '../../../../../modules/modules/nf-core/ashlar/main.nf' addParams( options: [args: '--flip-mosaic-x'] )
 
 def TEST_IMG = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-0{6,7}.ome.tiff"
 def TEST_IMG_1 = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-06.ome.tiff"
@@ -21,8 +19,6 @@ workflow test_ashlar {
     ASHLAR ( input_channel )
 }
 
-// we can add additional test workflows below
-
 include { INPUT_CHECK } from '../../../../../modules/modules/nf-core/ashlar/input_check.nf'
 
 workflow test_ashlar_sheet {

From afb2c27a6db292a63ea9dde7bda007121af081bc Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Fri, 9 Dec 2022 17:05:36 -0500
Subject: [PATCH 038/114] moved publishDir to test config as suggested by lint

---
 modules/nf-core/ashlar/main.nf               | 2 --
 tests/modules/nf-core/ashlar/nextflow.config | 2 ++
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 1abb41cc344..6662fcd1f9e 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -3,8 +3,6 @@ params.options = [:]
 options = initOptions(params.options)
 
 process ASHLAR {
-    publishDir = [ path: { "${params.outdir}/${meta.id}/" } ]
-
     tag '$meta.id'
     label 'process_single'
 
diff --git a/tests/modules/nf-core/ashlar/nextflow.config b/tests/modules/nf-core/ashlar/nextflow.config
index f4eedcfd783..86669d0389b 100644
--- a/tests/modules/nf-core/ashlar/nextflow.config
+++ b/tests/modules/nf-core/ashlar/nextflow.config
@@ -3,4 +3,6 @@ process {
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
     ext.args = "--flip-x"
+
+    publishDir = [ path: { "${params.outdir}/${meta.id}/" } ]
 }

From 2329c991d3a1fb0d764c7d1111aa65e48612772c Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Fri, 9 Dec 2022 17:35:47 -0500
Subject: [PATCH 039/114] removed initOptions; lint says deprecated; tests pass

---
 modules/nf-core/ashlar/functions.nf  | 10 ----------
 modules/nf-core/ashlar/main.nf       |  6 ------
 tests/modules/nf-core/ashlar/main.nf |  4 ++--
 3 files changed, 2 insertions(+), 18 deletions(-)
 delete mode 100644 modules/nf-core/ashlar/functions.nf

diff --git a/modules/nf-core/ashlar/functions.nf b/modules/nf-core/ashlar/functions.nf
deleted file mode 100644
index 3b25bddeddd..00000000000
--- a/modules/nf-core/ashlar/functions.nf
+++ /dev/null
@@ -1,10 +0,0 @@
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.publish_by_id   = args.publish_by_id ?: ''
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 6662fcd1f9e..fbead4bbc3a 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -1,7 +1,3 @@
-include { initOptions } from './functions'
-params.options = [:]
-options = initOptions(params.options)
-
 process ASHLAR {
     tag '$meta.id'
     label 'process_single'
@@ -24,14 +20,12 @@ process ASHLAR {
 
     script:
     def args_conf = task.ext.args ?: ''
-    def args_opt = options.args ?: ''
     def args_meta = meta.args ?: ''
 
     """
     ashlar \\
         $file_in \\
         $args_conf \\
-        $args_opt \\
         $args_meta
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index 1a83e3380a7..5079b524478 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -2,8 +2,8 @@
 
 nextflow.enable.dsl = 2
 
-// include { ASHLAR } from '../../../../../modules/modules/nf-core/ashlar/main.nf'
-include { ASHLAR } from '../../../../../modules/modules/nf-core/ashlar/main.nf' addParams( options: [args: '--flip-mosaic-x'] )
+include { ASHLAR } from '../../../../../modules/modules/nf-core/ashlar/main.nf'
+// include { ASHLAR } from '../../../../../modules/modules/nf-core/ashlar/main.nf' addParams( options: [args: '--flip-mosaic-x'] )
 
 def TEST_IMG = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-0{6,7}.ome.tiff"
 def TEST_IMG_1 = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-06.ome.tiff"

From 307d803e9fcd98055e48a12312589bee22afdc54 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Wed, 4 Jan 2023 15:39:29 -0500
Subject: [PATCH 040/114] multi-file row of test_1 failing, but others work

---
 tests/modules/nf-core/ashlar/main.nf | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index 5079b524478..dc77f5254c5 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -4,6 +4,7 @@ nextflow.enable.dsl = 2
 
 include { ASHLAR } from '../../../../../modules/modules/nf-core/ashlar/main.nf'
 // include { ASHLAR } from '../../../../../modules/modules/nf-core/ashlar/main.nf' addParams( options: [args: '--flip-mosaic-x'] )
+include { ZERO_UUID } from './zero_uuid.nf'
 
 def TEST_IMG = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-0{6,7}.ome.tiff"
 def TEST_IMG_1 = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-06.ome.tiff"
@@ -17,6 +18,9 @@ workflow test_ashlar {
     input_channel = Channel.fromList(input_list)
 
     ASHLAR ( input_channel )
+
+    ZERO_UUID ( ASHLAR.out[1] )
+
 }
 
 include { INPUT_CHECK } from '../../../../../modules/modules/nf-core/ashlar/input_check.nf'
@@ -37,4 +41,6 @@ workflow test_ashlar_sheet {
 
     ASHLAR ( input_maps )
 
+    ZERO_UUID ( ASHLAR.out[1] )
+
 }

From 2d5091c46781cdfec5ae0b955c2865000e414c83 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Mon, 9 Jan 2023 14:26:15 -0500
Subject: [PATCH 041/114] passes 3 tests with stable md5 sums

---
 tests/modules/nf-core/ashlar/main.nf | 38 +++++++++++++++-------------
 1 file changed, 20 insertions(+), 18 deletions(-)

diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index dc77f5254c5..99e7da6466d 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -3,18 +3,18 @@
 nextflow.enable.dsl = 2
 
 include { ASHLAR } from '../../../../../modules/modules/nf-core/ashlar/main.nf'
-// include { ASHLAR } from '../../../../../modules/modules/nf-core/ashlar/main.nf' addParams( options: [args: '--flip-mosaic-x'] )
 include { ZERO_UUID } from './zero_uuid.nf'
 
 def TEST_IMG = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-0{6,7}.ome.tiff"
 def TEST_IMG_1 = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-06.ome.tiff"
 def TEST_IMG_2 = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-07.ome.tiff"
-def TEST_SHEET = '/home/pollen/github/modules/tests/modules/nf-core/ashlar/input_sheet.csv'
+def TEST_DFP_1 = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/illumination/exemplar-001-cycle-06-dfp.ome.tiff"
+def TEST_FFP_1 = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/illumination/exemplar-001-cycle-06-ffp.ome.tiff"
 
-workflow test_ashlar {
+workflow test_ashlar_one_file {
 
-    input_list =  [ [ [ id:'test', args: '--flip-y' ],
-               "${TEST_IMG_1} ${TEST_IMG_2}" ] ]
+    input_list =  [ [ [ id:'test_1', args: '--flip-y' ],
+               "${TEST_IMG_1}" ] ]
     input_channel = Channel.fromList(input_list)
 
     ASHLAR ( input_channel )
@@ -23,23 +23,25 @@ workflow test_ashlar {
 
 }
 
-include { INPUT_CHECK } from '../../../../../modules/modules/nf-core/ashlar/input_check.nf'
+workflow test_ashlar_two_files {
 
-workflow test_ashlar_sheet {
+    input_list =  [ [ [ id:'test_2', args: '--flip-x' ],
+               "${TEST_IMG_1} ${TEST_IMG_2}" ] ]
+    input_channel = Channel.fromList(input_list)
 
-    ch_input = file(TEST_SHEET)
+    ASHLAR ( input_channel )
 
-    INPUT_CHECK (
-        ch_input
-    )
-    .images
-    .map {
-        it -> [ [ id: it.sample, args: '--flip-y' ],
-                it.file_list ]
-    }
-    .set { input_maps }
+    ZERO_UUID ( ASHLAR.out[1] )
 
-    ASHLAR ( input_maps )
+}
+
+workflow test_ashlar_align_channel {
+
+    input_list =  [ [ [ id:'test_1', args: '--align-channel 1' ],
+               "${TEST_IMG_1}" ] ]
+    input_channel = Channel.fromList(input_list)
+
+    ASHLAR ( input_channel )
 
     ZERO_UUID ( ASHLAR.out[1] )
 

From bbfa6131684ca7a05714f2e2b32fc96ce681b647 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Tue, 10 Jan 2023 11:34:27 -0500
Subject: [PATCH 042/114] clean-up and changed back to uuid block zero out
 instead of while loop; added exception check

---
 tests/modules/nf-core/ashlar/main.nf | 17 +++++++++++++++--
 1 file changed, 15 insertions(+), 2 deletions(-)

diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index 99e7da6466d..f5758d32619 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -3,13 +3,14 @@
 nextflow.enable.dsl = 2
 
 include { ASHLAR } from '../../../../../modules/modules/nf-core/ashlar/main.nf'
+// we zero out the UUID of output tiff images with ZERO_UUID so we get a consistent md5sum
 include { ZERO_UUID } from './zero_uuid.nf'
 
 def TEST_IMG = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-0{6,7}.ome.tiff"
 def TEST_IMG_1 = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-06.ome.tiff"
 def TEST_IMG_2 = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-07.ome.tiff"
-def TEST_DFP_1 = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/illumination/exemplar-001-cycle-06-dfp.ome.tiff"
-def TEST_FFP_1 = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/illumination/exemplar-001-cycle-06-ffp.ome.tiff"
+def TEST_DFP_1 = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/illumination/exemplar-001-cycle-06-dfp.tif"
+def TEST_FFP_1 = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/illumination/exemplar-001-cycle-06-ffp.tif"
 
 workflow test_ashlar_one_file {
 
@@ -46,3 +47,15 @@ workflow test_ashlar_align_channel {
     ZERO_UUID ( ASHLAR.out[1] )
 
 }
+
+workflow test_ashlar_dfp_ffp {
+
+    input_list =  [ [ [ id:'test_1', args: "--dfp ${TEST_DFP_1} --ffp ${TEST_FFP_1}" ],
+               "${TEST_IMG_1}" ] ]
+    input_channel = Channel.fromList(input_list)
+
+    ASHLAR ( input_channel )
+
+    ZERO_UUID ( ASHLAR.out[1] )
+
+}

From edc499845446e071f44d329fe6b9577c728e6fcd Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Tue, 10 Jan 2023 13:27:27 -0500
Subject: [PATCH 043/114] removed test publishDir for sample sheets

---
 tests/modules/nf-core/ashlar/nextflow.config | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/modules/nf-core/ashlar/nextflow.config b/tests/modules/nf-core/ashlar/nextflow.config
index 86669d0389b..581f49321e5 100644
--- a/tests/modules/nf-core/ashlar/nextflow.config
+++ b/tests/modules/nf-core/ashlar/nextflow.config
@@ -4,5 +4,4 @@ process {
 
     ext.args = "--flip-x"
 
-    publishDir = [ path: { "${params.outdir}/${meta.id}/" } ]
 }

From 12ad5dfe7ed5119b06f7bd33004296244caf5cb2 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Tue, 10 Jan 2023 15:57:06 -0500
Subject: [PATCH 044/114] clean-up

---
 modules/nf-core/ashlar/main.nf | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index fbead4bbc3a..683417d1a1d 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -3,11 +3,15 @@ process ASHLAR {
     label 'process_single'
 
     conda (params.enable_conda ? "bioconda::ashlar=1.17.0" : null)
-    // TODO nf-core: need to have this added
+    /* TODO nf-core: we'll provide a dockerfile as described in 5) under Software Requirements
+                     at https://nf-co.re/developers/modules#software-requirements
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ashlar':
         'quay.io/biocontainers/ashlar' }"
 
+    container 'ghcr.io/????/ashlar:1.17.0'
+    */
+
     input:
     tuple val(meta), val(file_in)
 

From eea6c46c4d5e5a0409ba89762c433dbe060114fd Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Tue, 10 Jan 2023 15:58:03 -0500
Subject: [PATCH 045/114] added Dockerfile

---
 modules/nf-core/ashlar/Dockerfile | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 modules/nf-core/ashlar/Dockerfile

diff --git a/modules/nf-core/ashlar/Dockerfile b/modules/nf-core/ashlar/Dockerfile
new file mode 100644
index 00000000000..b042410b45d
--- /dev/null
+++ b/modules/nf-core/ashlar/Dockerfile
@@ -0,0 +1,27 @@
+FROM ubuntu:22.04
+
+RUN apt-get update \
+    && DEBIAN_FRONTEND=noninteractive apt-get install -y \
+        build-essential \
+        ffmpeg \
+        git \
+        openjdk-11-jdk-headless \
+        python3-dev \
+        python3-pip \
+        python3-tk \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN pip3 install -q -U \
+    numpy \
+    pip
+
+COPY / /app/ashlar/
+RUN pip3 install /app/ashlar
+
+ENV OMP_NUM_THREADS 1
+
+VOLUME /data
+VOLUME /data2
+VOLUME /data3
+
+WORKDIR /data

From ba68c8e2e934da7261e7840ba4fdb82db80c686f Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Wed, 11 Jan 2023 13:15:42 -0500
Subject: [PATCH 046/114] clean-up

---
 .nf-core.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.nf-core.yml b/.nf-core.yml
index 723a978c789..006ca37ecb6 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -8,3 +8,4 @@ bump-versions:
   rseqc/inferexperiment: False
   rseqc/innerdistance: False
   sortmerna: False
+org_path: nf-core

From 9996fa7e12e5fb6c1711818918c74dd047957ed5 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Fri, 13 Jan 2023 12:50:26 -0500
Subject: [PATCH 047/114] updated to correct DOI

---
 modules/nf-core/ashlar/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/ashlar/meta.yml b/modules/nf-core/ashlar/meta.yml
index 58fa63c934c..a6dcd65a991 100644
--- a/modules/nf-core/ashlar/meta.yml
+++ b/modules/nf-core/ashlar/meta.yml
@@ -8,7 +8,7 @@ tools:
       description: "Alignment by Simultaneous Harmonization of Layer/Adjacency Registration"
       homepage: "https://labsyspharm.github.io/ashlar/"
       documentation: "https://labsyspharm.github.io/ashlar/"
-      doi: "10.1101/2021.04.20.440625"
+      doi: "10.1093/bioinformatics/btac544"
       licence: "['MIT']"
 
 input:

From c513dbba636a3f659e61321b8311fa949877fa5f Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Fri, 13 Jan 2023 13:45:21 -0500
Subject: [PATCH 048/114] added zero_uuid.nf

---
 tests/modules/nf-core/ashlar/zero_uuid.nf | 32 +++++++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100644 tests/modules/nf-core/ashlar/zero_uuid.nf

diff --git a/tests/modules/nf-core/ashlar/zero_uuid.nf b/tests/modules/nf-core/ashlar/zero_uuid.nf
new file mode 100644
index 00000000000..d7c2fb2fc5c
--- /dev/null
+++ b/tests/modules/nf-core/ashlar/zero_uuid.nf
@@ -0,0 +1,32 @@
+nextflow.enable.dsl=2
+
+process ZERO_UUID {
+
+    input:
+    each path(file_in)
+
+    script:
+    """
+    TARG_PATHS_ARRAY=(\$(find ../.. -name "ashlar_output.ome.tif" -printf "%k %p\n" | sort -n | awk -F ' ' '{print \$2}'))
+    TARG_ARRAY_LEN=\${#TARG_PATHS_ARRAY[@]}
+    if [[ \$(( \$TARG_ARRAY_LEN % 2 )) != 0 ]]; then
+        exit 0
+    fi
+
+    for (( idx=0; idx<\${TARG_ARRAY_LEN}; idx+=2 )); do
+        TARG_OFFSET=\$(cmp "\${TARG_PATHS_ARRAY[\$idx]}" "\${TARG_PATHS_ARRAY[\$idx+1]}" | awk -F ' ' '{print substr(\$5,1,length(\$5)-1)}')
+        if [ \$TARG_OFFSET ]; then
+            TARG_OFFSET="\$((TARG_OFFSET - 1))"
+            echo -n "00000000-0000-0000-0000-000000000000" | dd of=\${TARG_PATHS_ARRAY[\$idx]} bs=1 seek=\${TARG_OFFSET} conv=notrunc
+            echo -n "00000000-0000-0000-0000-000000000000" | dd of=\${TARG_PATHS_ARRAY[\$idx+1]} bs=1 seek=\${TARG_OFFSET} conv=notrunc
+        fi
+        TARG_OFFSET=\$(cmp "\${TARG_PATHS_ARRAY[\$idx]}" "\${TARG_PATHS_ARRAY[\$idx+1]}" | awk -F ' ' '{print substr(\$5,1,length(\$5)-1)}')
+        if [ \$TARG_OFFSET ]; then
+            echo "Error: files still different after UUID update!"
+        fi
+
+    done
+
+    """
+
+}

From 71b4be6d87b17c7f1a64d1dcf9fde79e2af99f12 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Fri, 13 Jan 2023 13:50:29 -0500
Subject: [PATCH 049/114] removed test sample sheet

---
 tests/modules/nf-core/ashlar/input_sheet.csv | 3 ---
 1 file changed, 3 deletions(-)
 delete mode 100644 tests/modules/nf-core/ashlar/input_sheet.csv

diff --git a/tests/modules/nf-core/ashlar/input_sheet.csv b/tests/modules/nf-core/ashlar/input_sheet.csv
deleted file mode 100644
index 43b4c1d4444..00000000000
--- a/tests/modules/nf-core/ashlar/input_sheet.csv
+++ /dev/null
@@ -1,3 +0,0 @@
-sample,file_list,args
-test_1,/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-06.ome.tiff /home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-07.ome.tiff,'--flip-mosaic-x'
-test_2,/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-08.ome.tiff,'--flip-mosaic-x'

From aff97c00a5ebd0e5bfb109424c5570067afd98a5 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Fri, 13 Jan 2023 14:44:20 -0500
Subject: [PATCH 050/114] changed input type to *.tif to match output type

---
 modules/nf-core/ashlar/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 683417d1a1d..69a222ab005 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -16,7 +16,7 @@ process ASHLAR {
     tuple val(meta), val(file_in)
 
     output:
-    tuple val(meta), path("*.ome.tif")  ,   emit: ashlar_tif
+    tuple val(meta), path("*.tif")  ,   emit: ashlar_tif
     path "versions.yml"                 ,   emit: versions
 
     when:

From 356f478bbfb960fd719abc01af623f79266e696b Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Fri, 13 Jan 2023 15:16:19 -0500
Subject: [PATCH 051/114] removed old test ashlar nextflow module

---
 modules/nf-core/ashlar/ashlar.nf | 92 --------------------------------
 1 file changed, 92 deletions(-)
 delete mode 100644 modules/nf-core/ashlar/ashlar.nf

diff --git a/modules/nf-core/ashlar/ashlar.nf b/modules/nf-core/ashlar/ashlar.nf
deleted file mode 100644
index 7e047d890aa..00000000000
--- a/modules/nf-core/ashlar/ashlar.nf
+++ /dev/null
@@ -1,92 +0,0 @@
-process wc {
-    input:
-        path file_in
-    output:
-        stdout
-
-    """
-        wc -l $file_in
-    """
-}
-
-process ashlar {
-    println 'running process ashlar in ashlar.nf'
-    conda 'bioconda::ashlar=1.17.0'
-    params.output = 'ashlar_output.ome.tif'
-    params.channel = '0'
-    params.flip_x = ''
-    params.flip_y = ''
-    params.flip_mosaic_x = ''
-    params.flip_mosaic_y = ''
-    params.maximum_shift = '15'
-    params.filter_sigma = ''
-    params.tile_size = '1024'
-    params.plates = ''
-    params.quiet = ''
-    params.help = ''
-    params.version = ''
-    params.output_channels = ''
-    params.ffp = ''
-    params.dfp = ''
-
-    input:
-        val file_in
-        val file_ffp
-        val file_dfp
-    output:
-        path '*.tif'
-
-    script:
-    def flip_x = params.flip_x == '' ? '' : '--flip-x'
-    def flip_y = params.flip_y == '' ? '' : '--flip-y'
-    def flip_mosaic_x = params.flip_mosaic_x == '' ? '' : '--flip-mosaic-x'
-    def flip_mosaic_y = params.flip_mosaic_y == '' ? '' : '--flip-mosaic-y'
-    def filter_sigma = params.filter_sigma == '' ? '' : '--filter-sigma ' + params.filter_sigma
-    def plates = params.plates == '' ? '' : '--plates'
-    def quiet = params.quiet == '' ? '' : '--quiet'
-    def help = params.help == '' ? false : true
-    def version = params.version == '' ? false : true
-    def output_channels = params.output_channels == '' ? '' : '--output-channels ' + params.output_channels
-    def ffp = params.ffp == '' ? '' : '--ffp ' + file_ffp
-    def dfp = params.dfp == '' ? '' : '--dfp ' + file_dfp
-
-    if(!help && !version) {
-        """
-        ashlar $file_in -o $params.output -c $params.channel $flip_x $flip_y $flip_mosaic_x $flip_mosaic_y -m $params.maximum_shift $filter_sigma --tile-size $params.tile_size $plates $quiet $output_channels $ffp $dfp
-        """
-    }
-    else if(help && version) {
-        """
-        echo 'Please select either the help or version input parameter, but not both.'
-        """
-    }
-    else if(help) {
-        """
-        ashlar --help
-        """
-    }
-    else if(version) {
-        """
-        ashlar --version
-        """
-    }
-    else {
-        """
-        ashlar --help
-        """
-    }
-}
-
-workflow {
-    input_file_list = params.in.split(',').join(' ')
-    ffp_file_list = []
-    if(params.ffp) {
-        ffp_file_list = params.ffp.split(',').join(' ')
-    }
-    dfp_file_list = []
-    if(params.dfp) {
-        dfp_file_list = params.dfp.split(',').join(' ')
-    }
-
-    ashlar(input_file_list, ffp_file_list, dfp_file_list) | wc | view { it.trim() }
-}

From c809ad48ae7a08ec6e737858a3f185a2c928dceb Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Fri, 13 Jan 2023 16:06:23 -0500
Subject: [PATCH 052/114] Update .nf-core.yml

removed added line from mistaken commit.
---
 .nf-core.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.nf-core.yml b/.nf-core.yml
index 006ca37ecb6..723a978c789 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -8,4 +8,3 @@ bump-versions:
   rseqc/inferexperiment: False
   rseqc/innerdistance: False
   sortmerna: False
-org_path: nf-core

From 14fb0dc832f4ac1a92b9251ddd370bf3b4a83eff Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Fri, 13 Jan 2023 18:21:23 -0500
Subject: [PATCH 053/114] restored formatting in pytest_modules.yml

---
 tests/config/pytest_modules.yml | 2920 +++++++++++++++----------------
 1 file changed, 1460 insertions(+), 1460 deletions(-)

diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index ef3f7c81b5b..df094b51a13 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1,2885 +1,2885 @@
 abacas:
-- modules/nf-core/abacas/**
-- tests/modules/nf-core/abacas/**
+  - modules/nf-core/abacas/**
+  - tests/modules/nf-core/abacas/**
 
 abricate/run:
-- modules/nf-core/abricate/run/**
-- tests/modules/nf-core/abricate/run/**
+  - modules/nf-core/abricate/run/**
+  - tests/modules/nf-core/abricate/run/**
 
 abricate/summary:
-- modules/nf-core/abricate/summary/**
-- tests/modules/nf-core/abricate/summary/**
+  - modules/nf-core/abricate/summary/**
+  - tests/modules/nf-core/abricate/summary/**
 
 adapterremoval:
-- modules/nf-core/adapterremoval/**
-- tests/modules/nf-core/adapterremoval/**
+  - modules/nf-core/adapterremoval/**
+  - tests/modules/nf-core/adapterremoval/**
 
 adapterremovalfixprefix:
-- modules/nf-core/adapterremovalfixprefix/**
-- tests/modules/nf-core/adapterremovalfixprefix/**
+  - modules/nf-core/adapterremovalfixprefix/**
+  - tests/modules/nf-core/adapterremovalfixprefix/**
 
 agrvate:
-- modules/nf-core/agrvate/**
-- tests/modules/nf-core/agrvate/**
+  - modules/nf-core/agrvate/**
+  - tests/modules/nf-core/agrvate/**
 
 allelecounter:
-- modules/nf-core/allelecounter/**
-- tests/modules/nf-core/allelecounter/**
+  - modules/nf-core/allelecounter/**
+  - tests/modules/nf-core/allelecounter/**
 
 ampir:
-- modules/nf-core/ampir/**
-- tests/modules/nf-core/ampir/**
+  - modules/nf-core/ampir/**
+  - tests/modules/nf-core/ampir/**
 
 amplify/predict:
-- modules/nf-core/amplify/predict/**
-- tests/modules/nf-core/amplify/predict/**
+  - modules/nf-core/amplify/predict/**
+  - tests/modules/nf-core/amplify/predict/**
 
 amps:
-- modules/nf-core/amps/**
-- tests/modules/nf-core/amps/**
+  - modules/nf-core/amps/**
+  - tests/modules/nf-core/amps/**
 
 amrfinderplus/run:
-- modules/nf-core/amrfinderplus/run/**
-- tests/modules/nf-core/amrfinderplus/run/**
+  - modules/nf-core/amrfinderplus/run/**
+  - tests/modules/nf-core/amrfinderplus/run/**
 
 amrfinderplus/update:
-- modules/nf-core/amrfinderplus/update/**
-- tests/modules/nf-core/amrfinderplus/update/**
+  - modules/nf-core/amrfinderplus/update/**
+  - tests/modules/nf-core/amrfinderplus/update/**
 
 angsd/docounts:
-- modules/nf-core/angsd/docounts/**
-- tests/modules/nf-core/angsd/docounts/**
+  - modules/nf-core/angsd/docounts/**
+  - tests/modules/nf-core/angsd/docounts/**
 
 antismash/antismashlite:
-- modules/nf-core/antismash/antismashlite/**
-- tests/modules/nf-core/antismash/antismashlite/**
+  - modules/nf-core/antismash/antismashlite/**
+  - tests/modules/nf-core/antismash/antismashlite/**
 
 antismash/antismashlitedownloaddatabases:
-- modules/nf-core/antismash/antismashlitedownloaddatabases/**
-- tests/modules/nf-core/antismash/antismashlitedownloaddatabases/**
+  - modules/nf-core/antismash/antismashlitedownloaddatabases/**
+  - tests/modules/nf-core/antismash/antismashlitedownloaddatabases/**
 
 aria2:
-- modules/nf-core/aria2/**
-- tests/modules/nf-core/aria2/**
+  - modules/nf-core/aria2/**
+  - tests/modules/nf-core/aria2/**
 
 ariba/getref:
-- modules/nf-core/ariba/getref/**
-- tests/modules/nf-core/ariba/getref/**
+  - modules/nf-core/ariba/getref/**
+  - tests/modules/nf-core/ariba/getref/**
 
 ariba/run:
-- modules/nf-core/ariba/run/**
-- tests/modules/nf-core/ariba/run/**
+  - modules/nf-core/ariba/run/**
+  - tests/modules/nf-core/ariba/run/**
 
 arriba:
-- modules/nf-core/arriba/**
-- tests/modules/nf-core/arriba/**
+  - modules/nf-core/arriba/**
+  - tests/modules/nf-core/arriba/**
 
 artic/guppyplex:
-- modules/nf-core/artic/guppyplex/**
-- tests/modules/nf-core/artic/guppyplex/**
+  - modules/nf-core/artic/guppyplex/**
+  - tests/modules/nf-core/artic/guppyplex/**
 
 artic/minion:
-- modules/nf-core/artic/minion/**
-- tests/modules/nf-core/artic/minion/**
+  - modules/nf-core/artic/minion/**
+  - tests/modules/nf-core/artic/minion/**
 
 ascat:
-- modules/nf-core/ascat/**
-- tests/modules/nf-core/ascat/**
+  - modules/nf-core/ascat/**
+  - tests/modules/nf-core/ascat/**
 
 ashlar:
-- modules/nf-core/ashlar/**
-- tests/modules/nf-core/ashlar/**
+  - modules/nf-core/ashlar/**
+  - tests/modules/nf-core/ashlar/**
 
 assemblyscan:
-- modules/nf-core/assemblyscan/**
-- tests/modules/nf-core/assemblyscan/**
+  - modules/nf-core/assemblyscan/**
+  - tests/modules/nf-core/assemblyscan/**
 
 ataqv/ataqv:
-- modules/nf-core/ataqv/ataqv/**
-- tests/modules/nf-core/ataqv/ataqv/**
+  - modules/nf-core/ataqv/ataqv/**
+  - tests/modules/nf-core/ataqv/ataqv/**
 
 ataqv/mkarv:
-- modules/nf-core/ataqv/mkarv/**
-- tests/modules/nf-core/ataqv/mkarv/**
+  - modules/nf-core/ataqv/mkarv/**
+  - tests/modules/nf-core/ataqv/mkarv/**
 
 atlas/call:
-- modules/nf-core/atlas/call/**
-- tests/modules/nf-core/atlas/call/**
+  - modules/nf-core/atlas/call/**
+  - tests/modules/nf-core/atlas/call/**
 
 atlas/pmd:
-- modules/nf-core/atlas/pmd/**
-- tests/modules/nf-core/atlas/pmd/**
+  - modules/nf-core/atlas/pmd/**
+  - tests/modules/nf-core/atlas/pmd/**
 
 atlas/recal:
-- modules/nf-core/atlas/recal/**
-- tests/modules/nf-core/atlas/recal/**
+  - modules/nf-core/atlas/recal/**
+  - tests/modules/nf-core/atlas/recal/**
 
 atlas/splitmerge:
-- modules/nf-core/atlas/splitmerge/**
-- tests/modules/nf-core/atlas/splitmerge/**
+  - modules/nf-core/atlas/splitmerge/**
+  - tests/modules/nf-core/atlas/splitmerge/**
 
 atlasgeneannotationmanipulation/gtf2featureannotation:
-- modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/**
-- tests/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/**
+  - modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/**
+  - tests/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/**
 
 bakta:
-- modules/nf-core/bakta/**
-- tests/modules/nf-core/bakta/**
+  - modules/nf-core/bakta/**
+  - tests/modules/nf-core/bakta/**
 
 bamaligncleaner:
-- modules/nf-core/bamaligncleaner/**
-- tests/modules/nf-core/bamaligncleaner/**
+  - modules/nf-core/bamaligncleaner/**
+  - tests/modules/nf-core/bamaligncleaner/**
 
 bamcmp:
-- modules/nf-core/bamcmp/**
-- tests/modules/nf-core/bamcmp/**
+  - modules/nf-core/bamcmp/**
+  - tests/modules/nf-core/bamcmp/**
 
 bamtools/convert:
-- modules/nf-core/bamtools/convert/**
-- tests/modules/nf-core/bamtools/convert/**
+  - modules/nf-core/bamtools/convert/**
+  - tests/modules/nf-core/bamtools/convert/**
 
 bamtools/split:
-- modules/nf-core/bamtools/split/**
-- tests/modules/nf-core/bamtools/split/**
+  - modules/nf-core/bamtools/split/**
+  - tests/modules/nf-core/bamtools/split/**
 
 bamtools/stats:
-- modules/nf-core/bamtools/stats/**
-- tests/modules/nf-core/bamtools/stats/**
+  - modules/nf-core/bamtools/stats/**
+  - tests/modules/nf-core/bamtools/stats/**
 
 bamutil/trimbam:
-- modules/nf-core/bamutil/trimbam/**
-- tests/modules/nf-core/bamutil/trimbam/**
+  - modules/nf-core/bamutil/trimbam/**
+  - tests/modules/nf-core/bamutil/trimbam/**
 
 bandage/image:
-- modules/nf-core/bandage/image/**
-- tests/modules/nf-core/bandage/image/**
+  - modules/nf-core/bandage/image/**
+  - tests/modules/nf-core/bandage/image/**
 
 bases2fastq:
-- modules/nf-core/bases2fastq/**
-- tests/modules/nf-core/bases2fastq/**
+  - modules/nf-core/bases2fastq/**
+  - tests/modules/nf-core/bases2fastq/**
 
 bbmap/align:
-- modules/nf-core/bbmap/align/**
-- tests/modules/nf-core/bbmap/align/**
+  - modules/nf-core/bbmap/align/**
+  - tests/modules/nf-core/bbmap/align/**
 
 bbmap/bbduk:
-- modules/nf-core/bbmap/bbduk/**
-- tests/modules/nf-core/bbmap/bbduk/**
+  - modules/nf-core/bbmap/bbduk/**
+  - tests/modules/nf-core/bbmap/bbduk/**
 
 bbmap/bbsplit:
-- modules/nf-core/bbmap/bbsplit/**
-- tests/modules/nf-core/bbmap/bbsplit/**
+  - modules/nf-core/bbmap/bbsplit/**
+  - tests/modules/nf-core/bbmap/bbsplit/**
 
 bbmap/clumpify:
-- modules/nf-core/bbmap/clumpify/**
-- tests/modules/nf-core/bbmap/clumpify/**
+  - modules/nf-core/bbmap/clumpify/**
+  - tests/modules/nf-core/bbmap/clumpify/**
 
 bbmap/index:
-- modules/nf-core/bbmap/index/**
-- tests/modules/nf-core/bbmap/index/**
+  - modules/nf-core/bbmap/index/**
+  - tests/modules/nf-core/bbmap/index/**
 
 bbmap/pileup:
-- modules/nf-core/bbmap/pileup/**
-- tests/modules/nf-core/bbmap/pileup/**
+  - modules/nf-core/bbmap/pileup/**
+  - tests/modules/nf-core/bbmap/pileup/**
 
 bcftools/annotate:
-- modules/nf-core/bcftools/annotate/**
-- tests/modules/nf-core/bcftools/annotate/**
+  - modules/nf-core/bcftools/annotate/**
+  - tests/modules/nf-core/bcftools/annotate/**
 
 bcftools/concat:
-- modules/nf-core/bcftools/concat/**
-- tests/modules/nf-core/bcftools/concat/**
+  - modules/nf-core/bcftools/concat/**
+  - tests/modules/nf-core/bcftools/concat/**
 
 bcftools/consensus:
-- modules/nf-core/bcftools/consensus/**
-- tests/modules/nf-core/bcftools/consensus/**
+  - modules/nf-core/bcftools/consensus/**
+  - tests/modules/nf-core/bcftools/consensus/**
 
 bcftools/convert:
-- modules/nf-core/bcftools/convert/**
-- tests/modules/nf-core/bcftools/convert/**
+  - modules/nf-core/bcftools/convert/**
+  - tests/modules/nf-core/bcftools/convert/**
 
 bcftools/filter:
-- modules/nf-core/bcftools/filter/**
-- tests/modules/nf-core/bcftools/filter/**
+  - modules/nf-core/bcftools/filter/**
+  - tests/modules/nf-core/bcftools/filter/**
 
 bcftools/index:
-- modules/nf-core/bcftools/index/**
-- tests/modules/nf-core/bcftools/index**
+  - modules/nf-core/bcftools/index/**
+  - tests/modules/nf-core/bcftools/index**
 
 bcftools/isec:
-- modules/nf-core/bcftools/isec/**
-- tests/modules/nf-core/bcftools/isec/**
+  - modules/nf-core/bcftools/isec/**
+  - tests/modules/nf-core/bcftools/isec/**
 
 bcftools/merge:
-- modules/nf-core/bcftools/merge/**
-- tests/modules/nf-core/bcftools/merge/**
+  - modules/nf-core/bcftools/merge/**
+  - tests/modules/nf-core/bcftools/merge/**
 
 bcftools/mpileup:
-- modules/nf-core/bcftools/mpileup/**
-- tests/modules/nf-core/bcftools/mpileup/**
+  - modules/nf-core/bcftools/mpileup/**
+  - tests/modules/nf-core/bcftools/mpileup/**
 
 bcftools/norm:
-- modules/nf-core/bcftools/norm/**
-- tests/modules/nf-core/bcftools/norm/**
+  - modules/nf-core/bcftools/norm/**
+  - tests/modules/nf-core/bcftools/norm/**
 
 bcftools/query:
-- modules/nf-core/bcftools/query/**
-- tests/modules/nf-core/bcftools/query/**
+  - modules/nf-core/bcftools/query/**
+  - tests/modules/nf-core/bcftools/query/**
 
 bcftools/reheader:
-- modules/nf-core/bcftools/reheader/**
-- tests/modules/nf-core/bcftools/reheader/**
+  - modules/nf-core/bcftools/reheader/**
+  - tests/modules/nf-core/bcftools/reheader/**
 
 bcftools/roh:
-- modules/nf-core/bcftools/roh/**
-- tests/modules/nf-core/bcftools/roh/**
+  - modules/nf-core/bcftools/roh/**
+  - tests/modules/nf-core/bcftools/roh/**
 
 bcftools/sort:
-- modules/nf-core/bcftools/sort/**
-- tests/modules/nf-core/bcftools/sort/**
+  - modules/nf-core/bcftools/sort/**
+  - tests/modules/nf-core/bcftools/sort/**
 
 bcftools/stats:
-- modules/nf-core/bcftools/stats/**
-- tests/modules/nf-core/bcftools/stats/**
+  - modules/nf-core/bcftools/stats/**
+  - tests/modules/nf-core/bcftools/stats/**
 
 bcftools/view:
-- modules/nf-core/bcftools/view/**
-- tests/modules/nf-core/bcftools/view/**
+  - modules/nf-core/bcftools/view/**
+  - tests/modules/nf-core/bcftools/view/**
 
 bcl2fastq:
-- modules/nf-core/bcl2fastq/**
-- tests/modules/nf-core/bcl2fastq/**
+  - modules/nf-core/bcl2fastq/**
+  - tests/modules/nf-core/bcl2fastq/**
 
 bclconvert:
-- modules/nf-core/bclconvert/**
-- tests/modules/nf-core/bclconvert/**
+  - modules/nf-core/bclconvert/**
+  - tests/modules/nf-core/bclconvert/**
 
 bedtools/bamtobed:
-- modules/nf-core/bedtools/bamtobed/**
-- tests/modules/nf-core/bedtools/bamtobed/**
+  - modules/nf-core/bedtools/bamtobed/**
+  - tests/modules/nf-core/bedtools/bamtobed/**
 
 bedtools/closest:
-- modules/nf-core/bedtools/closest/**
-- tests/modules/nf-core/bedtools/closest/**
+  - modules/nf-core/bedtools/closest/**
+  - tests/modules/nf-core/bedtools/closest/**
 
 bedtools/complement:
-- modules/nf-core/bedtools/complement/**
-- tests/modules/nf-core/bedtools/complement/**
+  - modules/nf-core/bedtools/complement/**
+  - tests/modules/nf-core/bedtools/complement/**
 
 bedtools/coverage:
-- modules/nf-core/bedtools/coverage/**
-- tests/modules/nf-core/bedtools/coverage/**
+  - modules/nf-core/bedtools/coverage/**
+  - tests/modules/nf-core/bedtools/coverage/**
 
 bedtools/genomecov:
-- modules/nf-core/bedtools/genomecov/**
-- tests/modules/nf-core/bedtools/genomecov/**
+  - modules/nf-core/bedtools/genomecov/**
+  - tests/modules/nf-core/bedtools/genomecov/**
 
 bedtools/getfasta:
-- modules/nf-core/bedtools/getfasta/**
-- tests/modules/nf-core/bedtools/getfasta/**
+  - modules/nf-core/bedtools/getfasta/**
+  - tests/modules/nf-core/bedtools/getfasta/**
 
 bedtools/intersect:
-- modules/nf-core/bedtools/intersect/**
-- tests/modules/nf-core/bedtools/intersect/**
+  - modules/nf-core/bedtools/intersect/**
+  - tests/modules/nf-core/bedtools/intersect/**
 
 bedtools/makewindows:
-- modules/nf-core/bedtools/makewindows/**
-- tests/modules/nf-core/bedtools/makewindows/**
+  - modules/nf-core/bedtools/makewindows/**
+  - tests/modules/nf-core/bedtools/makewindows/**
 
 bedtools/maskfasta:
-- modules/nf-core/bedtools/maskfasta/**
-- tests/modules/nf-core/bedtools/maskfasta/**
+  - modules/nf-core/bedtools/maskfasta/**
+  - tests/modules/nf-core/bedtools/maskfasta/**
 
 bedtools/merge:
-- modules/nf-core/bedtools/merge/**
-- tests/modules/nf-core/bedtools/merge/**
+  - modules/nf-core/bedtools/merge/**
+  - tests/modules/nf-core/bedtools/merge/**
 
 bedtools/slop:
-- modules/nf-core/bedtools/slop/**
-- tests/modules/nf-core/bedtools/slop/**
+  - modules/nf-core/bedtools/slop/**
+  - tests/modules/nf-core/bedtools/slop/**
 
 bedtools/sort:
-- modules/nf-core/bedtools/sort/**
-- tests/modules/nf-core/bedtools/sort/**
+  - modules/nf-core/bedtools/sort/**
+  - tests/modules/nf-core/bedtools/sort/**
 
 bedtools/split:
-- modules/nf-core/bedtools/split/**
-- tests/modules/nf-core/bedtools/split/**
+  - modules/nf-core/bedtools/split/**
+  - tests/modules/nf-core/bedtools/split/**
 
 bedtools/subtract:
-- modules/nf-core/bedtools/subtract/**
-- tests/modules/nf-core/bedtools/subtract/**
+  - modules/nf-core/bedtools/subtract/**
+  - tests/modules/nf-core/bedtools/subtract/**
 
 biobambam/bammarkduplicates2:
-- modules/nf-core/biobambam/bammarkduplicates2/**
-- tests/modules/nf-core/biobambam/bammarkduplicates2/**
+  - modules/nf-core/biobambam/bammarkduplicates2/**
+  - tests/modules/nf-core/biobambam/bammarkduplicates2/**
 
 biobambam/bammerge:
-- modules/nf-core/biobambam/bammerge/**
-- tests/modules/nf-core/biobambam/bammerge/**
+  - modules/nf-core/biobambam/bammerge/**
+  - tests/modules/nf-core/biobambam/bammerge/**
 
 biobambam/bamsormadup:
-- modules/nf-core/biobambam/bamsormadup/**
-- tests/modules/nf-core/biobambam/bamsormadup/**
+  - modules/nf-core/biobambam/bamsormadup/**
+  - tests/modules/nf-core/biobambam/bamsormadup/**
 
 biohansel:
-- modules/nf-core/biohansel/**
-- tests/modules/nf-core/biohansel/**
+  - modules/nf-core/biohansel/**
+  - tests/modules/nf-core/biohansel/**
 
 biscuit/align:
-- modules/nf-core/biscuit/index/**
-- modules/nf-core/biscuit/align/**
-- tests/modules/nf-core/biscuit/align/**
+  - modules/nf-core/biscuit/index/**
+  - modules/nf-core/biscuit/align/**
+  - tests/modules/nf-core/biscuit/align/**
 
 biscuit/biscuitblaster:
-- modules/nf-core/biscuit/index/**
-- modules/nf-core/biscuit/biscuitblaster/**
-- tests/modules/nf-core/biscuit/biscuitblaster/**
+  - modules/nf-core/biscuit/index/**
+  - modules/nf-core/biscuit/biscuitblaster/**
+  - tests/modules/nf-core/biscuit/biscuitblaster/**
 
 biscuit/bsconv:
-- modules/nf-core/biscuit/index/**
-- modules/nf-core/biscuit/bsconv/**
-- tests/modules/nf-core/biscuit/bsconv/**
+  - modules/nf-core/biscuit/index/**
+  - modules/nf-core/biscuit/bsconv/**
+  - tests/modules/nf-core/biscuit/bsconv/**
 
 biscuit/epiread:
-- modules/nf-core/biscuit/index/**
-- modules/nf-core/biscuit/epiread/**
-- tests/modules/nf-core/biscuit/epiread/**
+  - modules/nf-core/biscuit/index/**
+  - modules/nf-core/biscuit/epiread/**
+  - tests/modules/nf-core/biscuit/epiread/**
 
 biscuit/index:
-- modules/nf-core/biscuit/index/**
-- tests/modules/nf-core/biscuit/index/**
+  - modules/nf-core/biscuit/index/**
+  - tests/modules/nf-core/biscuit/index/**
 
 biscuit/mergecg:
-- modules/nf-core/biscuit/index/**
-- modules/nf-core/biscuit/mergecg/**
-- tests/modules/nf-core/biscuit/mergecg/**
+  - modules/nf-core/biscuit/index/**
+  - modules/nf-core/biscuit/mergecg/**
+  - tests/modules/nf-core/biscuit/mergecg/**
 
 biscuit/pileup:
-- modules/nf-core/biscuit/index/**
-- modules/nf-core/biscuit/pileup/**
-- tests/modules/nf-core/biscuit/pileup/**
+  - modules/nf-core/biscuit/index/**
+  - modules/nf-core/biscuit/pileup/**
+  - tests/modules/nf-core/biscuit/pileup/**
 
 biscuit/qc:
-- modules/nf-core/biscuit/index/**
-- modules/nf-core/biscuit/qc/**
-- tests/modules/nf-core/biscuit/qc/**
+  - modules/nf-core/biscuit/index/**
+  - modules/nf-core/biscuit/qc/**
+  - tests/modules/nf-core/biscuit/qc/**
 
 biscuit/vcf2bed:
-- modules/nf-core/biscuit/vcf2bed/**
-- tests/modules/nf-core/biscuit/vcf2bed/**
+  - modules/nf-core/biscuit/vcf2bed/**
+  - tests/modules/nf-core/biscuit/vcf2bed/**
 
 bismark/align:
-- modules/nf-core/bismark/align/**
-- modules/nf-core/bismark/genomepreparation/**
-- tests/modules/nf-core/bismark/align/**
+  - modules/nf-core/bismark/align/**
+  - modules/nf-core/bismark/genomepreparation/**
+  - tests/modules/nf-core/bismark/align/**
 
 bismark/deduplicate:
-- modules/nf-core/bismark/deduplicate/**
-- tests/modules/nf-core/bismark/deduplicate/**
+  - modules/nf-core/bismark/deduplicate/**
+  - tests/modules/nf-core/bismark/deduplicate/**
 
 bismark/genomepreparation:
-- modules/nf-core/bismark/genomepreparation/**
-- tests/modules/nf-core/bismark/genomepreparation/**
+  - modules/nf-core/bismark/genomepreparation/**
+  - tests/modules/nf-core/bismark/genomepreparation/**
 
 bismark/methylationextractor:
-- modules/nf-core/bismark/methylationextractor/**
-- modules/nf-core/bismark/genomepreparation/**
-- tests/modules/nf-core/bismark/methylationextractor/**
+  - modules/nf-core/bismark/methylationextractor/**
+  - modules/nf-core/bismark/genomepreparation/**
+  - tests/modules/nf-core/bismark/methylationextractor/**
 
 bismark/report:
-- modules/nf-core/bismark/genomepreparation/**
-- modules/nf-core/bismark/align/**
-- modules/nf-core/bismark/deduplicate/**
-- modules/nf-core/bismark/methylationextractor/**
-- modules/nf-core/bismark/report/**
-- tests/modules/nf-core/bismark/report/**
+  - modules/nf-core/bismark/genomepreparation/**
+  - modules/nf-core/bismark/align/**
+  - modules/nf-core/bismark/deduplicate/**
+  - modules/nf-core/bismark/methylationextractor/**
+  - modules/nf-core/bismark/report/**
+  - tests/modules/nf-core/bismark/report/**
 
 bismark/summary:
-- modules/nf-core/bismark/genomepreparation/**
-- modules/nf-core/bismark/align/**
-- modules/nf-core/bismark/deduplicate/**
-- modules/nf-core/bismark/methylationextractor/**
-- modules/nf-core/bismark/summary/**
-- tests/modules/nf-core/bismark/summary/**
+  - modules/nf-core/bismark/genomepreparation/**
+  - modules/nf-core/bismark/align/**
+  - modules/nf-core/bismark/deduplicate/**
+  - modules/nf-core/bismark/methylationextractor/**
+  - modules/nf-core/bismark/summary/**
+  - tests/modules/nf-core/bismark/summary/**
 
 blast/blastn:
-- modules/nf-core/blast/blastn/**
-- tests/modules/nf-core/blast/blastn/**
+  - modules/nf-core/blast/blastn/**
+  - tests/modules/nf-core/blast/blastn/**
 
 blast/makeblastdb:
-- modules/nf-core/blast/makeblastdb/**
-- tests/modules/nf-core/blast/makeblastdb/**
+  - modules/nf-core/blast/makeblastdb/**
+  - tests/modules/nf-core/blast/makeblastdb/**
 
 blast/tblastn:
-- modules/nf-core/blast/tblastn/**
-- tests/modules/nf-core/blast/tblastn/**
+  - modules/nf-core/blast/tblastn/**
+  - tests/modules/nf-core/blast/tblastn/**
 
 bowtie/align:
-- modules/nf-core/bowtie/align/**
-- modules/nf-core/bowtie/build/**
-- tests/modules/nf-core/bowtie/align/**
+  - modules/nf-core/bowtie/align/**
+  - modules/nf-core/bowtie/build/**
+  - tests/modules/nf-core/bowtie/align/**
 
 bowtie/build:
-- modules/nf-core/bowtie/build/**
-- tests/modules/nf-core/bowtie/build_test/**
+  - modules/nf-core/bowtie/build/**
+  - tests/modules/nf-core/bowtie/build_test/**
 
 bowtie2/align:
-- modules/nf-core/bowtie2/align/**
-- modules/nf-core/bowtie2/build/**
-- tests/modules/nf-core/bowtie2/align/**
+  - modules/nf-core/bowtie2/align/**
+  - modules/nf-core/bowtie2/build/**
+  - tests/modules/nf-core/bowtie2/align/**
 
 bowtie2/build:
-- modules/nf-core/bowtie2/build/**
-- tests/modules/nf-core/bowtie2/build_test/**
+  - modules/nf-core/bowtie2/build/**
+  - tests/modules/nf-core/bowtie2/build_test/**
 
 bracken/bracken:
-- modules/nf-core/bracken/bracken/**
-- tests/modules/nf-core/bracken/bracken/**
+  - modules/nf-core/bracken/bracken/**
+  - tests/modules/nf-core/bracken/bracken/**
 
 bracken/combinebrackenoutputs:
-- modules/nf-core/bracken/combinebrackenoutputs/**
-- tests/modules/nf-core/bracken/combinebrackenoutputs/**
+  - modules/nf-core/bracken/combinebrackenoutputs/**
+  - tests/modules/nf-core/bracken/combinebrackenoutputs/**
 
 busco:
-- modules/nf-core/busco/**
-- tests/modules/nf-core/busco/**
+  - modules/nf-core/busco/**
+  - tests/modules/nf-core/busco/**
 
 bwa/aln:
-- modules/nf-core/bwa/aln/**
-- tests/modules/nf-core/bwa/aln/**
+  - modules/nf-core/bwa/aln/**
+  - tests/modules/nf-core/bwa/aln/**
 
 bwa/index:
-- modules/nf-core/bwa/index/**
-- tests/modules/nf-core/bwa/index/**
+  - modules/nf-core/bwa/index/**
+  - tests/modules/nf-core/bwa/index/**
 
 bwa/mem:
-- modules/nf-core/bwa/mem/**
-- tests/modules/nf-core/bwa/mem/**
+  - modules/nf-core/bwa/mem/**
+  - tests/modules/nf-core/bwa/mem/**
 
 bwa/sampe:
-- modules/nf-core/bwa/sampe/**
-- tests/modules/nf-core/bwa/sampe/**
+  - modules/nf-core/bwa/sampe/**
+  - tests/modules/nf-core/bwa/sampe/**
 
 bwa/samse:
-- modules/nf-core/bwa/samse/**
-- tests/modules/nf-core/bwa/samse/**
+  - modules/nf-core/bwa/samse/**
+  - tests/modules/nf-core/bwa/samse/**
 
 bwamem2/index:
-- modules/nf-core/bwamem2/index/**
-- tests/modules/nf-core/bwamem2/index/**
+  - modules/nf-core/bwamem2/index/**
+  - tests/modules/nf-core/bwamem2/index/**
 
 bwamem2/mem:
-- modules/nf-core/bwamem2/mem/**
-- tests/modules/nf-core/bwamem2/mem/**
+  - modules/nf-core/bwamem2/mem/**
+  - tests/modules/nf-core/bwamem2/mem/**
 
 bwameth/align:
-- modules/nf-core/bwameth/align/**
-- tests/modules/nf-core/bwameth/align/**
+  - modules/nf-core/bwameth/align/**
+  - tests/modules/nf-core/bwameth/align/**
 
 bwameth/index:
-- modules/nf-core/bwameth/index/**
-- tests/modules/nf-core/bwameth/index/**
+  - modules/nf-core/bwameth/index/**
+  - tests/modules/nf-core/bwameth/index/**
 
 calder2:
-- modules/nf-core/calder2/**
-- tests/modules/nf-core/calder2/**
+  - modules/nf-core/calder2/**
+  - tests/modules/nf-core/calder2/**
 
 cat/cat:
-- modules/nf-core/cat/cat/**
-- tests/modules/nf-core/cat/cat/**
+  - modules/nf-core/cat/cat/**
+  - tests/modules/nf-core/cat/cat/**
 
 cat/fastq:
-- modules/nf-core/cat/fastq/**
-- tests/modules/nf-core/cat/fastq/**
+  - modules/nf-core/cat/fastq/**
+  - tests/modules/nf-core/cat/fastq/**
 
 cellranger/count:
-- modules/nf-core/cellranger/count/**
-- tests/modules/nf-core/cellranger/count/**
-- modules/nf-core/cellranger/mkref/**
-- tests/modules/nf-core/cellranger/mkref/**
-- modules/nf-core/cellranger/gtf/**
-- tests/modules/nf-core/cellranger/gtf/**
+  - modules/nf-core/cellranger/count/**
+  - tests/modules/nf-core/cellranger/count/**
+  - modules/nf-core/cellranger/mkref/**
+  - tests/modules/nf-core/cellranger/mkref/**
+  - modules/nf-core/cellranger/gtf/**
+  - tests/modules/nf-core/cellranger/gtf/**
 
 cellranger/gtf:
-- modules/nf-core/cellranger/gtf/**
-- tests/modules/nf-core/cellranger/gtf/**
+  - modules/nf-core/cellranger/gtf/**
+  - tests/modules/nf-core/cellranger/gtf/**
 
 cellranger/mkfastq:
-- modules/nf-core/cellranger/mkfastq/**
-- tests/modules/nf-core/cellranger/mkfastq/**
+  - modules/nf-core/cellranger/mkfastq/**
+  - tests/modules/nf-core/cellranger/mkfastq/**
 
 cellranger/mkgtf:
-- modules/nf-core/cellranger/mkgtf/**
-- tests/modules/nf-core/cellranger/mkgtf/**
+  - modules/nf-core/cellranger/mkgtf/**
+  - tests/modules/nf-core/cellranger/mkgtf/**
 
 cellranger/mkref:
-- modules/nf-core/cellranger/mkref/**
-- tests/modules/nf-core/cellranger/mkref/**
-- modules/nf-core/cellranger/gtf/**
-- tests/modules/nf-core/cellranger/gtf/**
+  - modules/nf-core/cellranger/mkref/**
+  - tests/modules/nf-core/cellranger/mkref/**
+  - modules/nf-core/cellranger/gtf/**
+  - tests/modules/nf-core/cellranger/gtf/**
 
 centrifuge/centrifuge:
-- modules/nf-core/centrifuge/centrifuge/**
-- tests/modules/nf-core/centrifuge/centrifuge/**
+  - modules/nf-core/centrifuge/centrifuge/**
+  - tests/modules/nf-core/centrifuge/centrifuge/**
 
 checkm/lineagewf:
-- modules/nf-core/checkm/lineagewf/**
-- tests/modules/nf-core/checkm/lineagewf/**
+  - modules/nf-core/checkm/lineagewf/**
+  - tests/modules/nf-core/checkm/lineagewf/**
 
 checkm/qa:
-- modules/nf-core/checkm/qa/**
-- tests/modules/nf-core/checkm/qa/**
+  - modules/nf-core/checkm/qa/**
+  - tests/modules/nf-core/checkm/qa/**
 
 chromap/chromap:
-- modules/nf-core/chromap/chromap/**
-- tests/modules/nf-core/chromap/chromap/**
+  - modules/nf-core/chromap/chromap/**
+  - tests/modules/nf-core/chromap/chromap/**
 
 chromap/index:
-- modules/nf-core/chromap/index/**
-- tests/modules/nf-core/chromap/index/**
+  - modules/nf-core/chromap/index/**
+  - tests/modules/nf-core/chromap/index/**
 
 circexplorer2/annotate:
-- modules/nf-core/circexplorer2/annotate/**
-- tests/modules/nf-core/circexplorer2/annotate/**
+  - modules/nf-core/circexplorer2/annotate/**
+  - tests/modules/nf-core/circexplorer2/annotate/**
 
 circexplorer2/parse:
-- modules/nf-core/circexplorer2/parse/**
-- tests/modules/nf-core/circexplorer2/parse/**
+  - modules/nf-core/circexplorer2/parse/**
+  - tests/modules/nf-core/circexplorer2/parse/**
 
 clonalframeml:
-- modules/nf-core/clonalframeml/**
-- tests/modules/nf-core/clonalframeml/**
+  - modules/nf-core/clonalframeml/**
+  - tests/modules/nf-core/clonalframeml/**
 
 cmseq/polymut:
-- modules/nf-core/cmseq/polymut/**
-- tests/modules/nf-core/cmseq/polymut/**
+  - modules/nf-core/cmseq/polymut/**
+  - tests/modules/nf-core/cmseq/polymut/**
 
 cnvkit/antitarget:
-- modules/nf-core/cnvkit/antitarget/**
-- tests/modules/nf-core/cnvkit/antitarget/**
+  - modules/nf-core/cnvkit/antitarget/**
+  - tests/modules/nf-core/cnvkit/antitarget/**
 
 cnvkit/batch:
-- modules/nf-core/cnvkit/batch/**
-- tests/modules/nf-core/cnvkit/batch/**
+  - modules/nf-core/cnvkit/batch/**
+  - tests/modules/nf-core/cnvkit/batch/**
 
 cnvkit/reference:
-- modules/nf-core/cnvkit/reference/**
-- tests/modules/nf-core/cnvkit/reference/**
+  - modules/nf-core/cnvkit/reference/**
+  - tests/modules/nf-core/cnvkit/reference/**
 
 concoct/concoct:
-- modules/nf-core/concoct/concoct/**
-- tests/modules/nf-core/concoct/concoct/**
+  - modules/nf-core/concoct/concoct/**
+  - tests/modules/nf-core/concoct/concoct/**
 
 concoct/concoctcoveragetable:
-- modules/nf-core/concoct/concoctcoveragetable/**
-- tests/modules/nf-core/concoct/concoctcoveragetable/**
+  - modules/nf-core/concoct/concoctcoveragetable/**
+  - tests/modules/nf-core/concoct/concoctcoveragetable/**
 
 concoct/cutupfasta:
-- modules/nf-core/concoct/cutupfasta/**
-- tests/modules/nf-core/concoct/cutupfasta/**
+  - modules/nf-core/concoct/cutupfasta/**
+  - tests/modules/nf-core/concoct/cutupfasta/**
 
 concoct/extractfastabins:
-- modules/nf-core/concoct/extractfastabins/**
-- tests/modules/nf-core/concoct/extractfastabins/**
+  - modules/nf-core/concoct/extractfastabins/**
+  - tests/modules/nf-core/concoct/extractfastabins/**
 
 concoct/mergecutupclustering:
-- modules/nf-core/concoct/mergecutupclustering/**
-- tests/modules/nf-core/concoct/mergecutupclustering/**
+  - modules/nf-core/concoct/mergecutupclustering/**
+  - tests/modules/nf-core/concoct/mergecutupclustering/**
 
 controlfreec/assesssignificance:
-- modules/nf-core/controlfreec/assesssignificance/**
-- tests/modules/nf-core/controlfreec/assesssignificance/**
+  - modules/nf-core/controlfreec/assesssignificance/**
+  - tests/modules/nf-core/controlfreec/assesssignificance/**
 
 controlfreec/freec:
-- modules/nf-core/controlfreec/freec/**
-- tests/modules/nf-core/controlfreec/freec/**
+  - modules/nf-core/controlfreec/freec/**
+  - tests/modules/nf-core/controlfreec/freec/**
 
 controlfreec/freec2bed:
-- modules/nf-core/controlfreec/freec2bed/**
-- tests/modules/nf-core/controlfreec/freec2bed/**
+  - modules/nf-core/controlfreec/freec2bed/**
+  - tests/modules/nf-core/controlfreec/freec2bed/**
 
 controlfreec/freec2circos:
-- modules/nf-core/controlfreec/freec2circos/**
-- tests/modules/nf-core/controlfreec/freec2circos/**
+  - modules/nf-core/controlfreec/freec2circos/**
+  - tests/modules/nf-core/controlfreec/freec2circos/**
 
 controlfreec/makegraph:
-- modules/nf-core/controlfreec/makegraph/**
-- tests/modules/nf-core/controlfreec/makegraph/**
+  - modules/nf-core/controlfreec/makegraph/**
+  - tests/modules/nf-core/controlfreec/makegraph/**
 
 cooler/cload:
-- modules/nf-core/cooler/cload/**
-- tests/modules/nf-core/cooler/cload/**
+  - modules/nf-core/cooler/cload/**
+  - tests/modules/nf-core/cooler/cload/**
 
 cooler/digest:
-- modules/nf-core/cooler/digest/**
-- tests/modules/nf-core/cooler/digest/**
+  - modules/nf-core/cooler/digest/**
+  - tests/modules/nf-core/cooler/digest/**
 
 cooler/dump:
-- modules/nf-core/cooler/dump/**
-- tests/modules/nf-core/cooler/dump/**
+  - modules/nf-core/cooler/dump/**
+  - tests/modules/nf-core/cooler/dump/**
 
 cooler/merge:
-- modules/nf-core/cooler/merge/**
-- tests/modules/nf-core/cooler/merge/**
+  - modules/nf-core/cooler/merge/**
+  - tests/modules/nf-core/cooler/merge/**
 
 cooler/zoomify:
-- modules/nf-core/cooler/zoomify/**
-- tests/software/cooler/zoomify/**
+  - modules/nf-core/cooler/zoomify/**
+  - tests/software/cooler/zoomify/**
 
 crumble:
-- modules/nf-core/crumble/**
-- tests/modules/nf-core/crumble/**
+  - modules/nf-core/crumble/**
+  - tests/modules/nf-core/crumble/**
 
 csvtk/concat:
-- modules/nf-core/csvtk/concat/**
-- tests/modules/nf-core/csvtk/concat/**
+  - modules/nf-core/csvtk/concat/**
+  - tests/modules/nf-core/csvtk/concat/**
 
 csvtk/split:
-- modules/nf-core/csvtk/split/**
-- tests/modules/nf-core/csvtk/split/**
+  - modules/nf-core/csvtk/split/**
+  - tests/modules/nf-core/csvtk/split/**
 
 custom/dumpsoftwareversions:
-- modules/nf-core/custom/dumpsoftwareversions/**
-- tests/modules/nf-core/custom/dumpsoftwareversions/**
+  - modules/nf-core/custom/dumpsoftwareversions/**
+  - tests/modules/nf-core/custom/dumpsoftwareversions/**
 
 custom/getchromsizes:
-- modules/nf-core/custom/getchromsizes/**
-- tests/modules/nf-core/custom/getchromsizes/**
+  - modules/nf-core/custom/getchromsizes/**
+  - tests/modules/nf-core/custom/getchromsizes/**
 
 custom/sratoolsncbisettings:
-- modules/nf-core/custom/sratoolsncbisettings/**
-- tests/modules/nf-core/custom/sratoolsncbisettings/**
+  - modules/nf-core/custom/sratoolsncbisettings/**
+  - tests/modules/nf-core/custom/sratoolsncbisettings/**
 
 cutadapt:
-- modules/nf-core/cutadapt/**
-- tests/modules/nf-core/cutadapt/**
+  - modules/nf-core/cutadapt/**
+  - tests/modules/nf-core/cutadapt/**
 
 damageprofiler:
-- modules/nf-core/damageprofiler/**
-- tests/modules/nf-core/damageprofiler/**
+  - modules/nf-core/damageprofiler/**
+  - tests/modules/nf-core/damageprofiler/**
 
 dastool/dastool:
-- modules/nf-core/dastool/dastool/**
-- tests/modules/nf-core/dastool/dastool/**
+  - modules/nf-core/dastool/dastool/**
+  - tests/modules/nf-core/dastool/dastool/**
 
 dastool/fastatocontig2bin:
-- modules/nf-core/dastool/fastatocontig2bin/**
-- tests/modules/nf-core/dastool/fastatocontig2bin/**
+  - modules/nf-core/dastool/fastatocontig2bin/**
+  - tests/modules/nf-core/dastool/fastatocontig2bin/**
 
 dastool/scaffolds2bin:
-- modules/nf-core/dastool/scaffolds2bin/**
-- tests/modules/nf-core/dastool/scaffolds2bin/**
+  - modules/nf-core/dastool/scaffolds2bin/**
+  - tests/modules/nf-core/dastool/scaffolds2bin/**
 
 dedup:
-- modules/nf-core/dedup/**
-- tests/modules/nf-core/dedup/**
+  - modules/nf-core/dedup/**
+  - tests/modules/nf-core/dedup/**
 
 deeparg/downloaddata:
-- modules/nf-core/deeparg/downloaddata/**
-- tests/modules/nf-core/deeparg/downloaddata/**
+  - modules/nf-core/deeparg/downloaddata/**
+  - tests/modules/nf-core/deeparg/downloaddata/**
 
 deeparg/predict:
-- modules/nf-core/deeparg/predict/**
-- tests/modules/nf-core/deeparg/predict/**
+  - modules/nf-core/deeparg/predict/**
+  - tests/modules/nf-core/deeparg/predict/**
 
 deepbgc/download:
-- modules/nf-core/deepbgc/download/**
-- tests/modules/nf-core/deepbgc/download/**
+  - modules/nf-core/deepbgc/download/**
+  - tests/modules/nf-core/deepbgc/download/**
 
 deepbgc/pipeline:
-- modules/nf-core/deepbgc/pipeline/**
-- tests/modules/nf-core/deepbgc/pipeline/**
+  - modules/nf-core/deepbgc/pipeline/**
+  - tests/modules/nf-core/deepbgc/pipeline/**
 
 deeptools/bamcoverage:
-- modules/nf-core/deeptools/bamcoverage/**
-- tests/modules/nf-core/deeptools/bamcoverage/**
+  - modules/nf-core/deeptools/bamcoverage/**
+  - tests/modules/nf-core/deeptools/bamcoverage/**
 
 deeptools/computematrix:
-- modules/nf-core/deeptools/computematrix/**
-- tests/modules/nf-core/deeptools/computematrix/**
+  - modules/nf-core/deeptools/computematrix/**
+  - tests/modules/nf-core/deeptools/computematrix/**
 
 deeptools/plotfingerprint:
-- modules/nf-core/deeptools/plotfingerprint/**
-- tests/modules/nf-core/deeptools/plotfingerprint/**
+  - modules/nf-core/deeptools/plotfingerprint/**
+  - tests/modules/nf-core/deeptools/plotfingerprint/**
 
 deeptools/plotheatmap:
-- modules/nf-core/deeptools/plotheatmap/**
-- tests/modules/nf-core/deeptools/plotheatmap/**
+  - modules/nf-core/deeptools/plotheatmap/**
+  - tests/modules/nf-core/deeptools/plotheatmap/**
 
 deeptools/plotprofile:
-- modules/nf-core/deeptools/plotprofile/**
-- tests/modules/nf-core/deeptools/plotprofile/**
+  - modules/nf-core/deeptools/plotprofile/**
+  - tests/modules/nf-core/deeptools/plotprofile/**
 
 deepvariant:
-- modules/nf-core/deepvariant/**
-- tests/modules/nf-core/deepvariant/**
+  - modules/nf-core/deepvariant/**
+  - tests/modules/nf-core/deepvariant/**
 
 delly/call:
-- modules/nf-core/delly/call/**
-- tests/modules/nf-core/delly/call/**
+  - modules/nf-core/delly/call/**
+  - tests/modules/nf-core/delly/call/**
 
 deseq2/differential:
-- modules/nf-core/deseq2/differential/**
-- tests/modules/nf-core/deseq2/differential/**
+  - modules/nf-core/deseq2/differential/**
+  - tests/modules/nf-core/deseq2/differential/**
 
 diamond/blastp:
-- modules/nf-core/diamond/blastp/**
-- tests/modules/nf-core/diamond/blastp/**
+  - modules/nf-core/diamond/blastp/**
+  - tests/modules/nf-core/diamond/blastp/**
 
 diamond/blastx:
-- modules/nf-core/diamond/blastx/**
-- tests/modules/nf-core/diamond/blastx/**
+  - modules/nf-core/diamond/blastx/**
+  - tests/modules/nf-core/diamond/blastx/**
 
 diamond/makedb:
-- modules/nf-core/diamond/makedb/**
-- tests/modules/nf-core/diamond/makedb/**
+  - modules/nf-core/diamond/makedb/**
+  - tests/modules/nf-core/diamond/makedb/**
 
 dragmap/align:
-- modules/nf-core/dragmap/align/**
-- tests/modules/nf-core/dragmap/align/**
+  - modules/nf-core/dragmap/align/**
+  - tests/modules/nf-core/dragmap/align/**
 
 dragmap/hashtable:
-- modules/nf-core/dragmap/hashtable/**
-- tests/modules/nf-core/dragmap/hashtable/**
+  - modules/nf-core/dragmap/hashtable/**
+  - tests/modules/nf-core/dragmap/hashtable/**
 
 dragonflye:
-- modules/nf-core/dragonflye/**
-- tests/modules/nf-core/dragonflye/**
+  - modules/nf-core/dragonflye/**
+  - tests/modules/nf-core/dragonflye/**
 
 dshbio/exportsegments:
-- modules/nf-core/dshbio/exportsegments/**
-- tests/modules/nf-core/dshbio/exportsegments/**
+  - modules/nf-core/dshbio/exportsegments/**
+  - tests/modules/nf-core/dshbio/exportsegments/**
 
 dshbio/filterbed:
-- modules/nf-core/dshbio/filterbed/**
-- tests/modules/nf-core/dshbio/filterbed/**
+  - modules/nf-core/dshbio/filterbed/**
+  - tests/modules/nf-core/dshbio/filterbed/**
 
 dshbio/filtergff3:
-- modules/nf-core/dshbio/filtergff3/**
-- tests/modules/nf-core/dshbio/filtergff3/**
+  - modules/nf-core/dshbio/filtergff3/**
+  - tests/modules/nf-core/dshbio/filtergff3/**
 
 dshbio/splitbed:
-- modules/nf-core/dshbio/splitbed/**
-- tests/modules/nf-core/dshbio/splitbed/**
+  - modules/nf-core/dshbio/splitbed/**
+  - tests/modules/nf-core/dshbio/splitbed/**
 
 dshbio/splitgff3:
-- modules/nf-core/dshbio/splitgff3/**
-- tests/modules/nf-core/dshbio/splitgff3/**
+  - modules/nf-core/dshbio/splitgff3/**
+  - tests/modules/nf-core/dshbio/splitgff3/**
 
 duphold:
-- modules/nf-core/duphold/**
-- tests/modules/nf-core/duphold/**
+  - modules/nf-core/duphold/**
+  - tests/modules/nf-core/duphold/**
 
 ectyper:
-- modules/nf-core/ectyper/**
-- tests/modules/nf-core/ectyper/**
+  - modules/nf-core/ectyper/**
+  - tests/modules/nf-core/ectyper/**
 
 eido/convert:
-- modules/nf-core/eido/convert/**
-- tests/modules/nf-core/eido/convert/**
+  - modules/nf-core/eido/convert/**
+  - tests/modules/nf-core/eido/convert/**
 
 eido/validate:
-- modules/nf-core/eido/validate/**
-- tests/modules/nf-core/eido/validate/**
+  - modules/nf-core/eido/validate/**
+  - tests/modules/nf-core/eido/validate/**
 
 elprep/filter:
-- modules/nf-core/elprep/filter/**
-- tests/modules/nf-core/elprep/filter/**
+  - modules/nf-core/elprep/filter/**
+  - tests/modules/nf-core/elprep/filter/**
 
 elprep/merge:
-- modules/nf-core/elprep/merge/**
-- tests/modules/nf-core/elprep/merge/**
+  - modules/nf-core/elprep/merge/**
+  - tests/modules/nf-core/elprep/merge/**
 
 elprep/split:
-- modules/nf-core/elprep/split/**
-- tests/modules/nf-core/elprep/split/**
+  - modules/nf-core/elprep/split/**
+  - tests/modules/nf-core/elprep/split/**
 
 emboss/seqret:
-- modules/nf-core/emboss/seqret/**
-- tests/modules/nf-core/emboss/seqret/**
+  - modules/nf-core/emboss/seqret/**
+  - tests/modules/nf-core/emboss/seqret/**
 
 emmtyper:
-- modules/nf-core/emmtyper/**
-- tests/modules/nf-core/emmtyper/**
+  - modules/nf-core/emmtyper/**
+  - tests/modules/nf-core/emmtyper/**
 
 endorspy:
-- modules/nf-core/endorspy/**
-- tests/modules/nf-core/endorspy/**
+  - modules/nf-core/endorspy/**
+  - tests/modules/nf-core/endorspy/**
 
 ensemblvep:
-- modules/nf-core/ensemblvep/**
-- tests/modules/nf-core/ensemblvep/**
+  - modules/nf-core/ensemblvep/**
+  - tests/modules/nf-core/ensemblvep/**
 
 entrezdirect/esearch:
-- modules/nf-core/entrezdirect/esearch/**
-- tests/modules/nf-core/entrezdirect/esearch/**
+  - modules/nf-core/entrezdirect/esearch/**
+  - tests/modules/nf-core/entrezdirect/esearch/**
 
 entrezdirect/esummary:
-- modules/nf-core/entrezdirect/esummary/**
-- tests/modules/nf-core/entrezdirect/esummary/**
+  - modules/nf-core/entrezdirect/esummary/**
+  - tests/modules/nf-core/entrezdirect/esummary/**
 
 entrezdirect/xtract:
-- modules/nf-core/entrezdirect/xtract/**
-- tests/modules/nf-core/entrezdirect/xtract/**
+  - modules/nf-core/entrezdirect/xtract/**
+  - tests/modules/nf-core/entrezdirect/xtract/**
 
 epang:
-- modules/nf-core/epang/**
-- tests/modules/nf-core/epang/
+  - modules/nf-core/epang/**
+  - tests/modules/nf-core/epang/
 
 expansionhunter:
-- modules/nf-core/expansionhunter/**
-- tests/modules/nf-core/expansionhunter/**
+  - modules/nf-core/expansionhunter/**
+  - tests/modules/nf-core/expansionhunter/**
 
 expansionhunterdenovo/merge:
-- modules/nf-core/expansionhunterdenovo/merge/**
-- tests/modules/nf-core/expansionhunterdenovo/merge/**
+  - modules/nf-core/expansionhunterdenovo/merge/**
+  - tests/modules/nf-core/expansionhunterdenovo/merge/**
 
 expansionhunterdenovo/profile:
-- modules/nf-core/expansionhunterdenovo/profile/**
-- tests/modules/nf-core/expansionhunterdenovo/profile/**
+  - modules/nf-core/expansionhunterdenovo/profile/**
+  - tests/modules/nf-core/expansionhunterdenovo/profile/**
 
 falco:
-- modules/nf-core/falco/**
-- tests/modules/nf-core/falco/**
+  - modules/nf-core/falco/**
+  - tests/modules/nf-core/falco/**
 
 faqcs:
-- modules/nf-core/faqcs/**
-- tests/modules/nf-core/faqcs/**
+  - modules/nf-core/faqcs/**
+  - tests/modules/nf-core/faqcs/**
 
 fargene:
-- modules/nf-core/fargene/**
-- tests/modules/nf-core/fargene/**
+  - modules/nf-core/fargene/**
+  - tests/modules/nf-core/fargene/**
 
 fastani:
-- modules/nf-core/fastani/**
-- tests/modules/nf-core/fastani/**
+  - modules/nf-core/fastani/**
+  - tests/modules/nf-core/fastani/**
 
 fastawindows:
-- modules/nf-core/fastawindows/**
-- tests/modules/nf-core/fastawindows/**
+  - modules/nf-core/fastawindows/**
+  - tests/modules/nf-core/fastawindows/**
 
 fastk/fastk:
-- modules/nf-core/fastk/fastk/**
-- tests/modules/nf-core/fastk/fastk/**
+  - modules/nf-core/fastk/fastk/**
+  - tests/modules/nf-core/fastk/fastk/**
 
 fastk/histex:
-- modules/nf-core/fastk/histex/**
-- tests/modules/nf-core/fastk/histex/**
+  - modules/nf-core/fastk/histex/**
+  - tests/modules/nf-core/fastk/histex/**
 
 fastk/merge:
-- modules/nf-core/fastk/merge/**
-- tests/modules/nf-core/fastk/merge/**
+  - modules/nf-core/fastk/merge/**
+  - tests/modules/nf-core/fastk/merge/**
 
 fastp:
-- modules/nf-core/fastp/**
-- tests/modules/nf-core/fastp/**
+  - modules/nf-core/fastp/**
+  - tests/modules/nf-core/fastp/**
 
 fastqc:
-- modules/nf-core/fastqc/**
-- tests/modules/nf-core/fastqc/**
+  - modules/nf-core/fastqc/**
+  - tests/modules/nf-core/fastqc/**
 
 fastqscan:
-- modules/nf-core/fastqscan/**
-- tests/modules/nf-core/fastqscan/**
+  - modules/nf-core/fastqscan/**
+  - tests/modules/nf-core/fastqscan/**
 
 fasttree:
-- modules/nf-core/fasttree/**
-- tests/modules/nf-core/fasttree/**
+  - modules/nf-core/fasttree/**
+  - tests/modules/nf-core/fasttree/**
 
 fcs/fcsadaptor:
-- modules/nf-core/fcs/fcsadaptor/**
-- tests/modules/nf-core/fcs/fcsadaptor/**
+  - modules/nf-core/fcs/fcsadaptor/**
+  - tests/modules/nf-core/fcs/fcsadaptor/**
 
 ffq:
-- modules/nf-core/ffq/**
-- tests/modules/nf-core/ffq/**
+  - modules/nf-core/ffq/**
+  - tests/modules/nf-core/ffq/**
 
 fgbio/callduplexconsensusreads:
-- modules/nf-core/fgbio/callduplexconsensusreads/**
-- tests/modules/nf-core/fgbio/callduplexconsensusreads/**
+  - modules/nf-core/fgbio/callduplexconsensusreads/**
+  - tests/modules/nf-core/fgbio/callduplexconsensusreads/**
 
 fgbio/callmolecularconsensusreads:
-- modules/nf-core/fgbio/callmolecularconsensusreads/**
-- tests/modules/nf-core/fgbio/callmolecularconsensusreads/**
+  - modules/nf-core/fgbio/callmolecularconsensusreads/**
+  - tests/modules/nf-core/fgbio/callmolecularconsensusreads/**
 
 fgbio/fastqtobam:
-- modules/nf-core/fgbio/fastqtobam/**
-- tests/modules/nf-core/fgbio/fastqtobam/**
+  - modules/nf-core/fgbio/fastqtobam/**
+  - tests/modules/nf-core/fgbio/fastqtobam/**
 
 fgbio/filterconsensusreads:
-- modules/nf-core/fgbio/filterconsensusreads/**
-- tests/modules/nf-core/fgbio/filterconsensusreads/**
+  - modules/nf-core/fgbio/filterconsensusreads/**
+  - tests/modules/nf-core/fgbio/filterconsensusreads/**
 
 fgbio/groupreadsbyumi:
-- modules/nf-core/fgbio/groupreadsbyumi/**
-- tests/modules/nf-core/fgbio/groupreadsbyumi/**
+  - modules/nf-core/fgbio/groupreadsbyumi/**
+  - tests/modules/nf-core/fgbio/groupreadsbyumi/**
 
 fgbio/sortbam:
-- modules/nf-core/fgbio/sortbam/**
-- tests/modules/nf-core/fgbio/sortbam/**
+  - modules/nf-core/fgbio/sortbam/**
+  - tests/modules/nf-core/fgbio/sortbam/**
 
 fgbio/zipperbams:
-- modules/nf-core/fgbio/zipperbams/**
-- tests/modules/nf-core/fgbio/zipperbams/**
+  - modules/nf-core/fgbio/zipperbams/**
+  - tests/modules/nf-core/fgbio/zipperbams/**
 
 filtlong:
-- modules/nf-core/filtlong/**
-- tests/modules/nf-core/filtlong/**
+  - modules/nf-core/filtlong/**
+  - tests/modules/nf-core/filtlong/**
 
 flash:
-- modules/nf-core/flash/**
-- tests/modules/nf-core/flash/**
+  - modules/nf-core/flash/**
+  - tests/modules/nf-core/flash/**
 
 flye:
-- modules/nf-core/flye/**
-- tests/modules/nf-core/flye/**
+  - modules/nf-core/flye/**
+  - tests/modules/nf-core/flye/**
 
 fq/lint:
-- modules/nf-core/fq/lint/**
-- tests/modules/nf-core/fq/lint/**
+  - modules/nf-core/fq/lint/**
+  - tests/modules/nf-core/fq/lint/**
 
 freebayes:
-- modules/nf-core/freebayes/**
-- tests/modules/nf-core/freebayes/**
+  - modules/nf-core/freebayes/**
+  - tests/modules/nf-core/freebayes/**
 
 gamma/gamma:
-- modules/nf-core/gamma/gamma/**
-- tests/modules/nf-core/gamma/gamma/**
+  - modules/nf-core/gamma/gamma/**
+  - tests/modules/nf-core/gamma/gamma/**
 
 gangstr:
-- modules/nf-core/gangstr/**
-- tests/modules/nf-core/gangstr/**
+  - modules/nf-core/gangstr/**
+  - tests/modules/nf-core/gangstr/**
 
 gappa/examineassign:
-- modules/nf-core/gappa/examineassign/**
-- tests/modules/nf-core/gappa/examineassign/**
+  - modules/nf-core/gappa/examineassign/**
+  - tests/modules/nf-core/gappa/examineassign/**
 
 gappa/examinegraft:
-- modules/nf-core/gappa/examinegraft/**
-- tests/modules/nf-core/gappa/examinegraft/**
+  - modules/nf-core/gappa/examinegraft/**
+  - tests/modules/nf-core/gappa/examinegraft/**
 
 gappa/examineheattree:
-- modules/nf-core/gappa/examineheattree/**
-- tests/modules/nf-core/gappa/examineheattree/**
+  - modules/nf-core/gappa/examineheattree/**
+  - tests/modules/nf-core/gappa/examineheattree/**
 
 gatk/indelrealigner:
-- modules/nf-core/gatk/indelrealigner/**
-- tests/modules/nf-core/gatk/indelrealigner/**
+  - modules/nf-core/gatk/indelrealigner/**
+  - tests/modules/nf-core/gatk/indelrealigner/**
 
 gatk/realignertargetcreator:
-- modules/nf-core/gatk/realignertargetcreator/**
-- tests/modules/nf-core/gatk/realignertargetcreator/**
+  - modules/nf-core/gatk/realignertargetcreator/**
+  - tests/modules/nf-core/gatk/realignertargetcreator/**
 
 gatk/unifiedgenotyper:
-- modules/nf-core/gatk/unifiedgenotyper/**
-- tests/modules/nf-core/gatk/unifiedgenotyper/**
+  - modules/nf-core/gatk/unifiedgenotyper/**
+  - tests/modules/nf-core/gatk/unifiedgenotyper/**
 
 gatk4/applybqsr:
-- modules/nf-core/gatk4/applybqsr/**
-- tests/modules/nf-core/gatk4/applybqsr/**
+  - modules/nf-core/gatk4/applybqsr/**
+  - tests/modules/nf-core/gatk4/applybqsr/**
 
 gatk4/applybqsrspark:
-- modules/nf-core/gatk4/applybqsrspark/**
-- tests/modules/nf-core/gatk4/applybqsrspark/**
+  - modules/nf-core/gatk4/applybqsrspark/**
+  - tests/modules/nf-core/gatk4/applybqsrspark/**
 
 gatk4/applyvqsr:
-- modules/nf-core/gatk4/applyvqsr/**
-- tests/modules/nf-core/gatk4/applyvqsr/**
+  - modules/nf-core/gatk4/applyvqsr/**
+  - tests/modules/nf-core/gatk4/applyvqsr/**
 
 gatk4/baserecalibrator:
-- modules/nf-core/gatk4/baserecalibrator/**
-- tests/modules/nf-core/gatk4/baserecalibrator/**
+  - modules/nf-core/gatk4/baserecalibrator/**
+  - tests/modules/nf-core/gatk4/baserecalibrator/**
 
 gatk4/baserecalibratorspark:
-- modules/nf-core/gatk4/baserecalibratorspark/**
-- tests/modules/nf-core/gatk4/baserecalibratorspark/**
+  - modules/nf-core/gatk4/baserecalibratorspark/**
+  - tests/modules/nf-core/gatk4/baserecalibratorspark/**
 
 gatk4/bedtointervallist:
-- modules/nf-core/gatk4/bedtointervallist/**
-- tests/modules/nf-core/gatk4/bedtointervallist/**
+  - modules/nf-core/gatk4/bedtointervallist/**
+  - tests/modules/nf-core/gatk4/bedtointervallist/**
 
 gatk4/calculatecontamination:
-- modules/nf-core/gatk4/calculatecontamination/**
-- tests/modules/nf-core/gatk4/calculatecontamination/**
+  - modules/nf-core/gatk4/calculatecontamination/**
+  - tests/modules/nf-core/gatk4/calculatecontamination/**
 
 gatk4/calibratedragstrmodel:
-- modules/nf-core/gatk4/calibratedragstrmodel/**
-- tests/modules/nf-core/gatk4/calibratedragstrmodel/**
+  - modules/nf-core/gatk4/calibratedragstrmodel/**
+  - tests/modules/nf-core/gatk4/calibratedragstrmodel/**
 
 gatk4/cnnscorevariants:
-- modules/nf-core/gatk4/cnnscorevariants/**
-- tests/modules/nf-core/gatk4/cnnscorevariants/**
+  - modules/nf-core/gatk4/cnnscorevariants/**
+  - tests/modules/nf-core/gatk4/cnnscorevariants/**
 
 gatk4/collectreadcounts:
-- modules/nf-core/gatk4/collectreadcounts/**
-- tests/modules/nf-core/gatk4/collectreadcounts/**
+  - modules/nf-core/gatk4/collectreadcounts/**
+  - tests/modules/nf-core/gatk4/collectreadcounts/**
 
 gatk4/collectsvevidence:
-- modules/nf-core/gatk4/collectsvevidence/**
-- tests/modules/nf-core/gatk4/collectsvevidence/**
+  - modules/nf-core/gatk4/collectsvevidence/**
+  - tests/modules/nf-core/gatk4/collectsvevidence/**
 
 gatk4/combinegvcfs:
-- modules/nf-core/gatk4/combinegvcfs/**
-- tests/modules/nf-core/gatk4/combinegvcfs/**
+  - modules/nf-core/gatk4/combinegvcfs/**
+  - tests/modules/nf-core/gatk4/combinegvcfs/**
 
 gatk4/composestrtablefile:
-- modules/nf-core/gatk4/composestrtablefile/**
-- tests/modules/nf-core/gatk4/composestrtablefile/**
+  - modules/nf-core/gatk4/composestrtablefile/**
+  - tests/modules/nf-core/gatk4/composestrtablefile/**
 
 gatk4/condensedepthevidence:
-- modules/nf-core/gatk4/condensedepthevidence/**
-- tests/modules/nf-core/gatk4/condensedepthevidence/**
+  - modules/nf-core/gatk4/condensedepthevidence/**
+  - tests/modules/nf-core/gatk4/condensedepthevidence/**
 
 gatk4/createsequencedictionary:
-- modules/nf-core/gatk4/createsequencedictionary/**
-- tests/modules/nf-core/gatk4/createsequencedictionary/**
+  - modules/nf-core/gatk4/createsequencedictionary/**
+  - tests/modules/nf-core/gatk4/createsequencedictionary/**
 
 gatk4/createsomaticpanelofnormals:
-- modules/nf-core/gatk4/createsomaticpanelofnormals/**
-- tests/modules/nf-core/gatk4/createsomaticpanelofnormals/**
+  - modules/nf-core/gatk4/createsomaticpanelofnormals/**
+  - tests/modules/nf-core/gatk4/createsomaticpanelofnormals/**
 
 gatk4/estimatelibrarycomplexity:
-- modules/nf-core/gatk4/estimatelibrarycomplexity/**
-- tests/modules/nf-core/gatk4/estimatelibrarycomplexity/**
+  - modules/nf-core/gatk4/estimatelibrarycomplexity/**
+  - tests/modules/nf-core/gatk4/estimatelibrarycomplexity/**
 
 gatk4/fastqtosam:
-- modules/nf-core/gatk4/fastqtosam/**
-- tests/modules/nf-core/gatk4/fastqtosam/**
+  - modules/nf-core/gatk4/fastqtosam/**
+  - tests/modules/nf-core/gatk4/fastqtosam/**
 
 gatk4/filtermutectcalls:
-- modules/nf-core/gatk4/filtermutectcalls/**
-- tests/modules/nf-core/gatk4/filtermutectcalls/**
+  - modules/nf-core/gatk4/filtermutectcalls/**
+  - tests/modules/nf-core/gatk4/filtermutectcalls/**
 
 gatk4/filtervarianttranches:
-- modules/nf-core/gatk4/filtervarianttranches/**
-- tests/modules/nf-core/gatk4/filtervarianttranches/**
+  - modules/nf-core/gatk4/filtervarianttranches/**
+  - tests/modules/nf-core/gatk4/filtervarianttranches/**
 
 gatk4/gatherbqsrreports:
-- modules/nf-core/gatk4/gatherbqsrreports/**
-- tests/modules/nf-core/gatk4/gatherbqsrreports/**
+  - modules/nf-core/gatk4/gatherbqsrreports/**
+  - tests/modules/nf-core/gatk4/gatherbqsrreports/**
 
 gatk4/gatherpileupsummaries:
-- modules/nf-core/gatk4/gatherpileupsummaries/**
-- tests/modules/nf-core/gatk4/gatherpileupsummaries/**
+  - modules/nf-core/gatk4/gatherpileupsummaries/**
+  - tests/modules/nf-core/gatk4/gatherpileupsummaries/**
 
 gatk4/genomicsdbimport:
-- modules/nf-core/gatk4/genomicsdbimport/**
-- tests/modules/nf-core/gatk4/genomicsdbimport/**
+  - modules/nf-core/gatk4/genomicsdbimport/**
+  - tests/modules/nf-core/gatk4/genomicsdbimport/**
 
 gatk4/genotypegvcfs:
-- modules/nf-core/gatk4/genotypegvcfs/**
-- tests/modules/nf-core/gatk4/genotypegvcfs/**
+  - modules/nf-core/gatk4/genotypegvcfs/**
+  - tests/modules/nf-core/gatk4/genotypegvcfs/**
 
 gatk4/getpileupsummaries:
-- modules/nf-core/gatk4/getpileupsummaries/**
-- tests/modules/nf-core/gatk4/getpileupsummaries/**
+  - modules/nf-core/gatk4/getpileupsummaries/**
+  - tests/modules/nf-core/gatk4/getpileupsummaries/**
 
 gatk4/haplotypecaller:
-- modules/nf-core/gatk4/haplotypecaller/**
-- tests/modules/nf-core/gatk4/haplotypecaller/**
+  - modules/nf-core/gatk4/haplotypecaller/**
+  - tests/modules/nf-core/gatk4/haplotypecaller/**
 
 gatk4/indexfeaturefile:
-- modules/nf-core/gatk4/indexfeaturefile/**
-- tests/modules/nf-core/gatk4/indexfeaturefile/**
+  - modules/nf-core/gatk4/indexfeaturefile/**
+  - tests/modules/nf-core/gatk4/indexfeaturefile/**
 
 gatk4/intervallisttobed:
-- modules/nf-core/gatk4/intervallisttobed/**
-- tests/modules/nf-core/gatk4/intervallisttobed/**
+  - modules/nf-core/gatk4/intervallisttobed/**
+  - tests/modules/nf-core/gatk4/intervallisttobed/**
 
 gatk4/intervallisttools:
-- modules/nf-core/gatk4/intervallisttools/**
-- tests/modules/nf-core/gatk4/intervallisttools/**
+  - modules/nf-core/gatk4/intervallisttools/**
+  - tests/modules/nf-core/gatk4/intervallisttools/**
 
 gatk4/learnreadorientationmodel:
-- modules/nf-core/gatk4/learnreadorientationmodel/**
-- tests/modules/nf-core/gatk4/learnreadorientationmodel/**
+  - modules/nf-core/gatk4/learnreadorientationmodel/**
+  - tests/modules/nf-core/gatk4/learnreadorientationmodel/**
 
 gatk4/leftalignandtrimvariants:
-- modules/nf-core/gatk4/leftalignandtrimvariants/**
-- tests/modules/nf-core/gatk4/leftalignandtrimvariants/**
+  - modules/nf-core/gatk4/leftalignandtrimvariants/**
+  - tests/modules/nf-core/gatk4/leftalignandtrimvariants/**
 
 gatk4/markduplicates:
-- modules/nf-core/gatk4/markduplicates/**
-- tests/modules/nf-core/gatk4/markduplicates/**
+  - modules/nf-core/gatk4/markduplicates/**
+  - tests/modules/nf-core/gatk4/markduplicates/**
 
 gatk4/markduplicatesspark:
-- modules/nf-core/gatk4/markduplicatesspark/**
-- tests/modules/nf-core/gatk4/markduplicatesspark/**
+  - modules/nf-core/gatk4/markduplicatesspark/**
+  - tests/modules/nf-core/gatk4/markduplicatesspark/**
 
 gatk4/mergebamalignment:
-- modules/nf-core/gatk4/mergebamalignment/**
-- tests/modules/nf-core/gatk4/mergebamalignment/**
+  - modules/nf-core/gatk4/mergebamalignment/**
+  - tests/modules/nf-core/gatk4/mergebamalignment/**
 
 gatk4/mergemutectstats:
-- modules/nf-core/gatk4/mergemutectstats/**
-- tests/modules/nf-core/gatk4/mergemutectstats/**
+  - modules/nf-core/gatk4/mergemutectstats/**
+  - tests/modules/nf-core/gatk4/mergemutectstats/**
 
 gatk4/mergevcfs:
-- modules/nf-core/gatk4/mergevcfs/**
-- tests/modules/nf-core/gatk4/mergevcfs/**
+  - modules/nf-core/gatk4/mergevcfs/**
+  - tests/modules/nf-core/gatk4/mergevcfs/**
 
 gatk4/mutect2:
-- modules/nf-core/gatk4/mutect2/**
-- tests/modules/nf-core/gatk4/mutect2/**
+  - modules/nf-core/gatk4/mutect2/**
+  - tests/modules/nf-core/gatk4/mutect2/**
 
 gatk4/printsvevidence:
-- modules/nf-core/gatk4/printsvevidence/**
-- tests/modules/nf-core/gatk4/printsvevidence/**
+  - modules/nf-core/gatk4/printsvevidence/**
+  - tests/modules/nf-core/gatk4/printsvevidence/**
 
 gatk4/reblockgvcf:
-- modules/nf-core/gatk4/reblockgvcf/**
-- tests/modules/nf-core/gatk4/reblockgvcf/**
+  - modules/nf-core/gatk4/reblockgvcf/**
+  - tests/modules/nf-core/gatk4/reblockgvcf/**
 
 gatk4/revertsam:
-- modules/nf-core/gatk4/revertsam/**
-- tests/modules/nf-core/gatk4/revertsam/**
+  - modules/nf-core/gatk4/revertsam/**
+  - tests/modules/nf-core/gatk4/revertsam/**
 
 gatk4/samtofastq:
-- modules/nf-core/gatk4/samtofastq/**
-- tests/modules/nf-core/gatk4/samtofastq/**
+  - modules/nf-core/gatk4/samtofastq/**
+  - tests/modules/nf-core/gatk4/samtofastq/**
 
 gatk4/selectvariants:
-- modules/nf-core/gatk4/selectvariants/**
-- tests/modules/nf-core/gatk4/selectvariants/**
+  - modules/nf-core/gatk4/selectvariants/**
+  - tests/modules/nf-core/gatk4/selectvariants/**
 
 gatk4/shiftfasta:
-- modules/nf-core/gatk4/shiftfasta/**
-- tests/modules/nf-core/gatk4/shiftfasta/**
+  - modules/nf-core/gatk4/shiftfasta/**
+  - tests/modules/nf-core/gatk4/shiftfasta/**
 
 gatk4/sitedepthtobaf:
-- modules/nf-core/gatk4/sitedepthtobaf/**
-- tests/modules/nf-core/gatk4/sitedepthtobaf/**
+  - modules/nf-core/gatk4/sitedepthtobaf/**
+  - tests/modules/nf-core/gatk4/sitedepthtobaf/**
 
 gatk4/splitintervals:
-- modules/nf-core/gatk4/splitintervals/**
-- tests/modules/nf-core/gatk4/splitintervals/**
+  - modules/nf-core/gatk4/splitintervals/**
+  - tests/modules/nf-core/gatk4/splitintervals/**
 
 gatk4/splitncigarreads:
-- modules/nf-core/gatk4/splitncigarreads/**
-- tests/modules/nf-core/gatk4/splitncigarreads/**
+  - modules/nf-core/gatk4/splitncigarreads/**
+  - tests/modules/nf-core/gatk4/splitncigarreads/**
 
 gatk4/svannotate:
-- modules/nf-core/gatk4/svannotate/**
-- tests/modules/nf-core/gatk4/svannotate/**
+  - modules/nf-core/gatk4/svannotate/**
+  - tests/modules/nf-core/gatk4/svannotate/**
 
 gatk4/svcluster:
-- modules/nf-core/gatk4/svcluster/**
-- tests/modules/nf-core/gatk4/svcluster/**
+  - modules/nf-core/gatk4/svcluster/**
+  - tests/modules/nf-core/gatk4/svcluster/**
 
 gatk4/variantfiltration:
-- modules/nf-core/gatk4/variantfiltration/**
-- tests/modules/nf-core/gatk4/variantfiltration/**
+  - modules/nf-core/gatk4/variantfiltration/**
+  - tests/modules/nf-core/gatk4/variantfiltration/**
 
 gatk4/variantrecalibrator:
-- modules/nf-core/gatk4/variantrecalibrator/**
-- tests/modules/nf-core/gatk4/variantrecalibrator/**
+  - modules/nf-core/gatk4/variantrecalibrator/**
+  - tests/modules/nf-core/gatk4/variantrecalibrator/**
 
 gecco/run:
-- modules/nf-core/gecco/run/**
-- tests/modules/nf-core/gecco/run/**
+  - modules/nf-core/gecco/run/**
+  - tests/modules/nf-core/gecco/run/**
 
 genescopefk:
-- modules/nf-core/genescopefk/**
-- tests/modules/nf-core/genescopefk/**
+  - modules/nf-core/genescopefk/**
+  - tests/modules/nf-core/genescopefk/**
 
 genmap/index:
-- modules/nf-core/genmap/index/**
-- tests/modules/nf-core/genmap/index/**
+  - modules/nf-core/genmap/index/**
+  - tests/modules/nf-core/genmap/index/**
 
 genmap/mappability:
-- modules/nf-core/genmap/mappability/**
-- tests/modules/nf-core/genmap/mappability/**
+  - modules/nf-core/genmap/mappability/**
+  - tests/modules/nf-core/genmap/mappability/**
 
 genmod/annotate:
-- modules/nf-core/genmod/annotate/**
-- tests/modules/nf-core/genmod/annotate/**
+  - modules/nf-core/genmod/annotate/**
+  - tests/modules/nf-core/genmod/annotate/**
 
 genmod/compound:
-- modules/nf-core/genmod/compound/**
-- tests/modules/nf-core/genmod/compound/**
+  - modules/nf-core/genmod/compound/**
+  - tests/modules/nf-core/genmod/compound/**
 
 genmod/models:
-- modules/nf-core/genmod/models/**
-- tests/modules/nf-core/genmod/models/**
+  - modules/nf-core/genmod/models/**
+  - tests/modules/nf-core/genmod/models/**
 
 genmod/score:
-- modules/nf-core/genmod/score/**
-- tests/modules/nf-core/genmod/score/**
+  - modules/nf-core/genmod/score/**
+  - tests/modules/nf-core/genmod/score/**
 
 genomescope2:
-- modules/nf-core/genomescope2/**
-- tests/modules/nf-core/genomescope2/**
+  - modules/nf-core/genomescope2/**
+  - tests/modules/nf-core/genomescope2/**
 
 genotyphi/parse:
-- modules/nf-core/genotyphi/parse/**
-- tests/modules/nf-core/genotyphi/parse/**
+  - modules/nf-core/genotyphi/parse/**
+  - tests/modules/nf-core/genotyphi/parse/**
 
 genrich:
-- modules/nf-core/genrich/**
-- tests/modules/nf-core/genrich/**
+  - modules/nf-core/genrich/**
+  - tests/modules/nf-core/genrich/**
 
 gfaffix:
-- modules/nf-core/gfaffix/**
-- tests/modules/nf-core/gfaffix/**
+  - modules/nf-core/gfaffix/**
+  - tests/modules/nf-core/gfaffix/**
 
 gffread:
-- modules/nf-core/gffread/**
-- tests/modules/nf-core/gffread/**
+  - modules/nf-core/gffread/**
+  - tests/modules/nf-core/gffread/**
 
 glimpse/chunk:
-- modules/nf-core/glimpse/chunk/**
-- tests/modules/nf-core/glimpse/chunk/**
+  - modules/nf-core/glimpse/chunk/**
+  - tests/modules/nf-core/glimpse/chunk/**
 
 glnexus:
-- modules/nf-core/glnexus/**
-- tests/modules/nf-core/glnexus/**
+  - modules/nf-core/glnexus/**
+  - tests/modules/nf-core/glnexus/**
 
 goat/taxonsearch:
-- modules/nf-core/goat/taxonsearch/**
-- tests/modules/nf-core/goat/taxonsearch/**
+  - modules/nf-core/goat/taxonsearch/**
+  - tests/modules/nf-core/goat/taxonsearch/**
 
 graphmap2/align:
-- modules/nf-core/graphmap2/align/**
-- tests/modules/nf-core/graphmap2/align/**
+  - modules/nf-core/graphmap2/align/**
+  - tests/modules/nf-core/graphmap2/align/**
 
 graphmap2/index:
-- modules/nf-core/graphmap2/index/**
-- tests/modules/nf-core/graphmap2/index/**
+  - modules/nf-core/graphmap2/index/**
+  - tests/modules/nf-core/graphmap2/index/**
 
 gstama/collapse:
-- modules/nf-core/gstama/collapse/**
-- tests/modules/nf-core/gstama/collapse/**
+  - modules/nf-core/gstama/collapse/**
+  - tests/modules/nf-core/gstama/collapse/**
 
 gstama/merge:
-- modules/nf-core/gstama/merge/**
-- tests/modules/nf-core/gstama/merge/**
+  - modules/nf-core/gstama/merge/**
+  - tests/modules/nf-core/gstama/merge/**
 
 gstama/polyacleanup:
-- modules/nf-core/gstama/polyacleanup/**
-- tests/modules/nf-core/gstama/polyacleanup/**
+  - modules/nf-core/gstama/polyacleanup/**
+  - tests/modules/nf-core/gstama/polyacleanup/**
 
 gtdbtk/classifywf:
-- modules/nf-core/gtdbtk/classifywf/**
-- tests/modules/nf-core/gtdbtk/classifywf/**
+  - modules/nf-core/gtdbtk/classifywf/**
+  - tests/modules/nf-core/gtdbtk/classifywf/**
 
 gubbins:
-- modules/nf-core/gubbins/**
-- tests/modules/nf-core/gubbins/**
+  - modules/nf-core/gubbins/**
+  - tests/modules/nf-core/gubbins/**
 
 gunc/downloaddb:
-- modules/nf-core/gunc/downloaddb/**
-- tests/modules/nf-core/gunc/downloaddb/**
+  - modules/nf-core/gunc/downloaddb/**
+  - tests/modules/nf-core/gunc/downloaddb/**
 
 gunc/run:
-- modules/nf-core/gunc/run/**
-- tests/modules/nf-core/gunc/run/**
+  - modules/nf-core/gunc/run/**
+  - tests/modules/nf-core/gunc/run/**
 
 gunzip:
-- modules/nf-core/gunzip/**
-- tests/modules/nf-core/gunzip/**
+  - modules/nf-core/gunzip/**
+  - tests/modules/nf-core/gunzip/**
 
 gvcftools/extractvariants:
-- modules/nf-core/gvcftools/extractvariants/**
-- tests/modules/nf-core/gvcftools/extractvariants/**
+  - modules/nf-core/gvcftools/extractvariants/**
+  - tests/modules/nf-core/gvcftools/extractvariants/**
 
 hamronization/abricate:
-- modules/nf-core/hamronization/abricate/**
-- tests/modules/nf-core/hamronization/abricate/**
+  - modules/nf-core/hamronization/abricate/**
+  - tests/modules/nf-core/hamronization/abricate/**
 
 hamronization/amrfinderplus:
-- modules/nf-core/hamronization/amrfinderplus/**
-- tests/modules/nf-core/hamronization/amrfinderplus/**
+  - modules/nf-core/hamronization/amrfinderplus/**
+  - tests/modules/nf-core/hamronization/amrfinderplus/**
 
 hamronization/deeparg:
-- modules/nf-core/hamronization/deeparg/**
-- tests/modules/nf-core/hamronization/deeparg/**
+  - modules/nf-core/hamronization/deeparg/**
+  - tests/modules/nf-core/hamronization/deeparg/**
 
 hamronization/fargene:
-- modules/nf-core/hamronization/fargene/**
-- tests/modules/nf-core/hamronization/fargene/**
+  - modules/nf-core/hamronization/fargene/**
+  - tests/modules/nf-core/hamronization/fargene/**
 
 hamronization/rgi:
-- modules/nf-core/hamronization/rgi/**
-- tests/modules/nf-core/hamronization/rgi/**
+  - modules/nf-core/hamronization/rgi/**
+  - tests/modules/nf-core/hamronization/rgi/**
 
 hamronization/summarize:
-- modules/nf-core/hamronization/summarize/**
-- tests/modules/nf-core/hamronization/summarize/**
+  - modules/nf-core/hamronization/summarize/**
+  - tests/modules/nf-core/hamronization/summarize/**
 
 hapibd:
-- modules/nf-core/hapibd/**
-- tests/modules/nf-core/hapibd/**
+  - modules/nf-core/hapibd/**
+  - tests/modules/nf-core/hapibd/**
 
 haplocheck:
-- modules/nf-core/haplocheck/**
-- tests/modules/nf-core/haplocheck/**
+  - modules/nf-core/haplocheck/**
+  - tests/modules/nf-core/haplocheck/**
 
 haplogrep2/classify:
-- modules/nf-core/haplogrep2/classify/**
-- tests/modules/nf-core/haplogrep2/classify/**
+  - modules/nf-core/haplogrep2/classify/**
+  - tests/modules/nf-core/haplogrep2/classify/**
 
 happy/happy:
-- modules/nf-core/happy/happy/**
-- tests/modules/nf-core/happy/happy/**
+  - modules/nf-core/happy/happy/**
+  - tests/modules/nf-core/happy/happy/**
 
 happy/prepy:
-- modules/nf-core/happy/prepy/**
-- tests/modules/nf-core/happy/prepy/**
+  - modules/nf-core/happy/prepy/**
+  - tests/modules/nf-core/happy/prepy/**
 
 hicap:
-- modules/nf-core/hicap/**
-- tests/modules/nf-core/hicap/**
+  - modules/nf-core/hicap/**
+  - tests/modules/nf-core/hicap/**
 
 hifiasm:
-- modules/nf-core/hifiasm/**
-- tests/modules/nf-core/hifiasm/**
+  - modules/nf-core/hifiasm/**
+  - tests/modules/nf-core/hifiasm/**
 
 hisat2/align:
-- modules/nf-core/hisat2/align/**
-- modules/nf-core/hisat2/build/**
-- modules/nf-core/hisat2/extractsplicesites/**
-- tests/modules/nf-core/hisat2/align/**
+  - modules/nf-core/hisat2/align/**
+  - modules/nf-core/hisat2/build/**
+  - modules/nf-core/hisat2/extractsplicesites/**
+  - tests/modules/nf-core/hisat2/align/**
 
 hisat2/build:
-- modules/nf-core/hisat2/build/**
-- modules/nf-core/hisat2/extractsplicesites/**
-- tests/modules/nf-core/hisat2/build_test/**
+  - modules/nf-core/hisat2/build/**
+  - modules/nf-core/hisat2/extractsplicesites/**
+  - tests/modules/nf-core/hisat2/build_test/**
 
 hisat2/extractsplicesites:
-- modules/nf-core/hisat2/extractsplicesites/**
-- tests/modules/nf-core/hisat2/extractsplicesites/**
+  - modules/nf-core/hisat2/extractsplicesites/**
+  - tests/modules/nf-core/hisat2/extractsplicesites/**
 
 hmmcopy/gccounter:
-- modules/nf-core/hmmcopy/gccounter/**
-- tests/modules/nf-core/hmmcopy/gccounter/**
+  - modules/nf-core/hmmcopy/gccounter/**
+  - tests/modules/nf-core/hmmcopy/gccounter/**
 
 hmmcopy/generatemap:
-- modules/nf-core/hmmcopy/generatemap/**
-- tests/modules/nf-core/hmmcopy/generatemap/**
+  - modules/nf-core/hmmcopy/generatemap/**
+  - tests/modules/nf-core/hmmcopy/generatemap/**
 
 hmmcopy/mapcounter:
-- modules/nf-core/hmmcopy/mapcounter/**
-- tests/modules/nf-core/hmmcopy/mapcounter/**
+  - modules/nf-core/hmmcopy/mapcounter/**
+  - tests/modules/nf-core/hmmcopy/mapcounter/**
 
 hmmcopy/readcounter:
-- modules/nf-core/hmmcopy/readcounter/**
-- tests/modules/nf-core/hmmcopy/readcounter/**
+  - modules/nf-core/hmmcopy/readcounter/**
+  - tests/modules/nf-core/hmmcopy/readcounter/**
 
 hmmer/eslalimask:
-- modules/nf-core/hmmer/eslalimask/**
-- tests/modules/nf-core/hmmer/eslalimask/**
+  - modules/nf-core/hmmer/eslalimask/**
+  - tests/modules/nf-core/hmmer/eslalimask/**
 
 hmmer/eslreformat:
-- modules/nf-core/hmmer/eslreformat/**
-- tests/modules/nf-core/hmmer/eslreformat/**
+  - modules/nf-core/hmmer/eslreformat/**
+  - tests/modules/nf-core/hmmer/eslreformat/**
 
 hmmer/hmmalign:
-- modules/nf-core/hmmer/hmmalign/**
-- tests/modules/nf-core/hmmer/hmmalign/**
+  - modules/nf-core/hmmer/hmmalign/**
+  - tests/modules/nf-core/hmmer/hmmalign/**
 
 hmmer/hmmbuild:
-- modules/nf-core/hmmer/hmmbuild/**
-- tests/modules/nf-core/hmmer/hmmbuild/**
+  - modules/nf-core/hmmer/hmmbuild/**
+  - tests/modules/nf-core/hmmer/hmmbuild/**
 
 hmmer/hmmsearch:
-- modules/nf-core/hmmer/hmmsearch/**
-- tests/modules/nf-core/hmmer/hmmsearch/**
+  - modules/nf-core/hmmer/hmmsearch/**
+  - tests/modules/nf-core/hmmer/hmmsearch/**
 
 hmtnote:
-- modules/nf-core/hmtnote/**
-- tests/modules/nf-core/hmtnote/**
+  - modules/nf-core/hmtnote/**
+  - tests/modules/nf-core/hmtnote/**
 
 homer/annotatepeaks:
-- modules/nf-core/homer/annotatepeaks/**
-- tests/modules/nf-core/homer/annotatepeaks/**
+  - modules/nf-core/homer/annotatepeaks/**
+  - tests/modules/nf-core/homer/annotatepeaks/**
 
 homer/findpeaks:
-- modules/nf-core/homer/findpeaks/**
-- modules/nf-core/homer/maketagdirectory/**
-- tests/modules/nf-core/homer/findpeaks/**
+  - modules/nf-core/homer/findpeaks/**
+  - modules/nf-core/homer/maketagdirectory/**
+  - tests/modules/nf-core/homer/findpeaks/**
 
 homer/maketagdirectory:
-- modules/nf-core/homer/maketagdirectory/**
-- tests/modules/nf-core/homer/maketagdirectory/**
+  - modules/nf-core/homer/maketagdirectory/**
+  - tests/modules/nf-core/homer/maketagdirectory/**
 
 homer/makeucscfile:
-- modules/nf-core/homer/makeucscfile/**
-- tests/modules/nf-core/homer/makeucscfile/**
+  - modules/nf-core/homer/makeucscfile/**
+  - tests/modules/nf-core/homer/makeucscfile/**
 
 homer/pos2bed:
-- modules/nf-core/homer/pos2bed/**
-- modules/nf-core/homer/maketagdirectory/**
-- modules/nf-core/homer/findpeaks/**
-- tests/modules/nf-core/homer/pos2bed/**
+  - modules/nf-core/homer/pos2bed/**
+  - modules/nf-core/homer/maketagdirectory/**
+  - modules/nf-core/homer/findpeaks/**
+  - tests/modules/nf-core/homer/pos2bed/**
 
 hpsuissero:
-- modules/nf-core/hpsuissero/**
-- tests/modules/nf-core/hpsuissero/**
+  - modules/nf-core/hpsuissero/**
+  - tests/modules/nf-core/hpsuissero/**
 
 ichorcna/createpon:
-- modules/nf-core/ichorcna/createpon/**
-- tests/modules/nf-core/ichorcna/createpon/**
+  - modules/nf-core/ichorcna/createpon/**
+  - tests/modules/nf-core/ichorcna/createpon/**
 
 ichorcna/run:
-- modules/nf-core/ichorcna/run/**
-- tests/modules/nf-core/ichorcna/run/**
+  - modules/nf-core/ichorcna/run/**
+  - tests/modules/nf-core/ichorcna/run/**
 
 idr:
-- modules/nf-core/idr/**
-- tests/modules/nf-core/idr/**
+  - modules/nf-core/idr/**
+  - tests/modules/nf-core/idr/**
 
 imputeme/vcftoprs:
-- modules/nf-core/imputeme/vcftoprs/**
-- tests/modules/nf-core/imputeme/vcftoprs/**
+  - modules/nf-core/imputeme/vcftoprs/**
+  - tests/modules/nf-core/imputeme/vcftoprs/**
 
 instrain/profile:
-- modules/nf-core/instrain/profile/**
-- tests/modules/nf-core/instrain/profile/**
+  - modules/nf-core/instrain/profile/**
+  - tests/modules/nf-core/instrain/profile/**
 
 iqtree:
-- modules/nf-core/iqtree/**
-- tests/modules/nf-core/iqtree/**
+  - modules/nf-core/iqtree/**
+  - tests/modules/nf-core/iqtree/**
 
 ismapper:
-- modules/nf-core/ismapper/**
-- tests/modules/nf-core/ismapper/**
+  - modules/nf-core/ismapper/**
+  - tests/modules/nf-core/ismapper/**
 
 isoseq3/cluster:
-- modules/nf-core/isoseq3/cluster/**
-- tests/modules/nf-core/isoseq3/cluster/**
+  - modules/nf-core/isoseq3/cluster/**
+  - tests/modules/nf-core/isoseq3/cluster/**
 
 isoseq3/refine:
-- modules/nf-core/isoseq3/refine/**
-- tests/modules/nf-core/isoseq3/refine/**
+  - modules/nf-core/isoseq3/refine/**
+  - tests/modules/nf-core/isoseq3/refine/**
 
 ivar/consensus:
-- modules/nf-core/ivar/consensus/**
-- tests/modules/nf-core/ivar/consensus/**
+  - modules/nf-core/ivar/consensus/**
+  - tests/modules/nf-core/ivar/consensus/**
 
 ivar/trim:
-- modules/nf-core/ivar/trim/**
-- tests/modules/nf-core/ivar/trim/**
+  - modules/nf-core/ivar/trim/**
+  - tests/modules/nf-core/ivar/trim/**
 
 ivar/variants:
-- modules/nf-core/ivar/variants/**
-- tests/modules/nf-core/ivar/variants/**
+  - modules/nf-core/ivar/variants/**
+  - tests/modules/nf-core/ivar/variants/**
 
 jupyternotebook:
-- modules/nf-core/jupyternotebook/**
-- tests/modules/nf-core/jupyternotebook/**
+  - modules/nf-core/jupyternotebook/**
+  - tests/modules/nf-core/jupyternotebook/**
 
 kaiju/kaiju:
-- modules/nf-core/kaiju/kaiju/**
-- tests/modules/nf-core/kaiju/kaiju/**
+  - modules/nf-core/kaiju/kaiju/**
+  - tests/modules/nf-core/kaiju/kaiju/**
 
 kaiju/kaiju2krona:
-- modules/nf-core/kaiju/kaiju2krona/**
-- tests/modules/nf-core/kaiju/kaiju2krona/**
+  - modules/nf-core/kaiju/kaiju2krona/**
+  - tests/modules/nf-core/kaiju/kaiju2krona/**
 
 kaiju/kaiju2table:
-- modules/nf-core/kaiju/kaiju2table/**
-- tests/modules/nf-core/kaiju/kaiju2table/**
+  - modules/nf-core/kaiju/kaiju2table/**
+  - tests/modules/nf-core/kaiju/kaiju2table/**
 
 kallisto/index:
-- modules/nf-core/kallisto/index/**
-- tests/modules/nf-core/kallisto/index/**
+  - modules/nf-core/kallisto/index/**
+  - tests/modules/nf-core/kallisto/index/**
 
 kallistobustools/count:
-- modules/nf-core/kallistobustools/count/**
-- tests/modules/nf-core/kallistobustools/count/**
+  - modules/nf-core/kallistobustools/count/**
+  - tests/modules/nf-core/kallistobustools/count/**
 
 kallistobustools/ref:
-- modules/nf-core/kallistobustools/ref/**
-- tests/modules/nf-core/kallistobustools/ref/**
+  - modules/nf-core/kallistobustools/ref/**
+  - tests/modules/nf-core/kallistobustools/ref/**
 
 kat/hist:
-- modules/nf-core/kat/hist/**
-- tests/modules/nf-core/kat/hist/**
+  - modules/nf-core/kat/hist/**
+  - tests/modules/nf-core/kat/hist/**
 
 khmer/normalizebymedian:
-- modules/nf-core/khmer/normalizebymedian/**
-- tests/modules/nf-core/khmer/normalizebymedian/**
+  - modules/nf-core/khmer/normalizebymedian/**
+  - tests/modules/nf-core/khmer/normalizebymedian/**
 
 khmer/uniquekmers:
-- modules/nf-core/khmer/uniquekmers/**
-- tests/modules/nf-core/khmer/uniquekmers/**
+  - modules/nf-core/khmer/uniquekmers/**
+  - tests/modules/nf-core/khmer/uniquekmers/**
 
 kleborate:
-- modules/nf-core/kleborate/**
-- tests/modules/nf-core/kleborate/**
+  - modules/nf-core/kleborate/**
+  - tests/modules/nf-core/kleborate/**
 
 kofamscan:
-- modules/nf-core/kofamscan/**
-- tests/modules/nf-core/kofamscan/**
+  - modules/nf-core/kofamscan/**
+  - tests/modules/nf-core/kofamscan/**
 
 kraken2/kraken2:
-- modules/nf-core/kraken2/kraken2/**
-- modules/nf-core/untar/**
-- tests/modules/nf-core/kraken2/kraken2/**
+  - modules/nf-core/kraken2/kraken2/**
+  - modules/nf-core/untar/**
+  - tests/modules/nf-core/kraken2/kraken2/**
 
 krakentools/combinekreports:
-- modules/nf-core/krakentools/combinekreports/**
-- tests/modules/nf-core/krakentools/combinekreports/**
+  - modules/nf-core/krakentools/combinekreports/**
+  - tests/modules/nf-core/krakentools/combinekreports/**
 
 krakentools/kreport2krona:
-- modules/nf-core/krakentools/kreport2krona/**
-- tests/modules/nf-core/krakentools/kreport2krona/**
+  - modules/nf-core/krakentools/kreport2krona/**
+  - tests/modules/nf-core/krakentools/kreport2krona/**
 
 krakenuniq/build:
-- modules/nf-core/krakenuniq/build/**
-- tests/modules/nf-core/krakenuniq/build/**
+  - modules/nf-core/krakenuniq/build/**
+  - tests/modules/nf-core/krakenuniq/build/**
 
 krakenuniq/download:
-- modules/nf-core/krakenuniq/download/**
-- tests/modules/nf-core/krakenuniq/download/**
+  - modules/nf-core/krakenuniq/download/**
+  - tests/modules/nf-core/krakenuniq/download/**
 
 krakenuniq/preloadedkrakenuniq:
-- modules/nf-core/krakenuniq/preloadedkrakenuniq/**
-- tests/modules/nf-core/krakenuniq/preloadedkrakenuniq/**
+  - modules/nf-core/krakenuniq/preloadedkrakenuniq/**
+  - tests/modules/nf-core/krakenuniq/preloadedkrakenuniq/**
 
 krona/kronadb:
-- modules/nf-core/krona/kronadb/**
-- tests/modules/nf-core/krona/kronadb/**
+  - modules/nf-core/krona/kronadb/**
+  - tests/modules/nf-core/krona/kronadb/**
 
 krona/ktimporttaxonomy:
-- modules/nf-core/krona/ktimporttaxonomy/**
-- tests/modules/nf-core/krona/ktimporttaxonomy/**
+  - modules/nf-core/krona/ktimporttaxonomy/**
+  - tests/modules/nf-core/krona/ktimporttaxonomy/**
 
 krona/ktimporttext:
-- modules/nf-core/krona/ktimporttext/**
-- tests/modules/nf-core/krona/ktimporttext/**
+  - modules/nf-core/krona/ktimporttext/**
+  - tests/modules/nf-core/krona/ktimporttext/**
 
 krona/ktupdatetaxonomy:
-- modules/nf-core/krona/ktupdatetaxonomy/**
-- tests/modules/nf-core/krona/ktupdatetaxonomy/**
+  - modules/nf-core/krona/ktupdatetaxonomy/**
+  - tests/modules/nf-core/krona/ktupdatetaxonomy/**
 
 last/dotplot:
-- modules/nf-core/last/dotplot/**
-- tests/modules/nf-core/last/dotplot/**
+  - modules/nf-core/last/dotplot/**
+  - tests/modules/nf-core/last/dotplot/**
 
 last/lastal:
-- modules/nf-core/last/lastal/**
-- tests/modules/nf-core/last/lastal/**
+  - modules/nf-core/last/lastal/**
+  - tests/modules/nf-core/last/lastal/**
 
 last/lastdb:
-- modules/nf-core/last/lastdb/**
-- tests/modules/nf-core/last/lastdb/**
+  - modules/nf-core/last/lastdb/**
+  - tests/modules/nf-core/last/lastdb/**
 
 last/mafconvert:
-- modules/nf-core/last/mafconvert/**
-- tests/modules/nf-core/last/mafconvert/**
+  - modules/nf-core/last/mafconvert/**
+  - tests/modules/nf-core/last/mafconvert/**
 
 last/mafswap:
-- modules/nf-core/last/mafswap/**
-- tests/modules/nf-core/last/mafswap/**
+  - modules/nf-core/last/mafswap/**
+  - tests/modules/nf-core/last/mafswap/**
 
 last/postmask:
-- modules/nf-core/last/postmask/**
-- tests/modules/nf-core/last/postmask/**
+  - modules/nf-core/last/postmask/**
+  - tests/modules/nf-core/last/postmask/**
 
 last/split:
-- modules/nf-core/last/split/**
-- tests/modules/nf-core/last/split/**
+  - modules/nf-core/last/split/**
+  - tests/modules/nf-core/last/split/**
 
 last/train:
-- modules/nf-core/last/train/**
-- tests/modules/nf-core/last/train/**
+  - modules/nf-core/last/train/**
+  - tests/modules/nf-core/last/train/**
 
 leehom:
-- modules/nf-core/leehom/**
-- tests/modules/nf-core/leehom/**
+  - modules/nf-core/leehom/**
+  - tests/modules/nf-core/leehom/**
 
 legsta:
-- modules/nf-core/legsta/**
-- tests/modules/nf-core/legsta/**
+  - modules/nf-core/legsta/**
+  - tests/modules/nf-core/legsta/**
 
 lima:
-- modules/nf-core/lima/**
-- tests/modules/nf-core/lima/**
+  - modules/nf-core/lima/**
+  - tests/modules/nf-core/lima/**
 
 lissero:
-- modules/nf-core/lissero/**
-- tests/modules/nf-core/lissero/**
+  - modules/nf-core/lissero/**
+  - tests/modules/nf-core/lissero/**
 
 lofreq/call:
-- modules/nf-core/lofreq/call/**
-- tests/modules/nf-core/lofreq/call/**
+  - modules/nf-core/lofreq/call/**
+  - tests/modules/nf-core/lofreq/call/**
 
 lofreq/callparallel:
-- modules/nf-core/lofreq/callparallel/**
-- tests/modules/nf-core/lofreq/callparallel/**
+  - modules/nf-core/lofreq/callparallel/**
+  - tests/modules/nf-core/lofreq/callparallel/**
 
 lofreq/filter:
-- modules/nf-core/lofreq/filter/**
-- tests/modules/nf-core/lofreq/filter/**
+  - modules/nf-core/lofreq/filter/**
+  - tests/modules/nf-core/lofreq/filter/**
 
 lofreq/indelqual:
-- modules/nf-core/lofreq/indelqual/**
-- tests/modules/nf-core/lofreq/indelqual/**
+  - modules/nf-core/lofreq/indelqual/**
+  - tests/modules/nf-core/lofreq/indelqual/**
 
 macrel/contigs:
-- modules/nf-core/macrel/contigs/**
-- tests/modules/nf-core/macrel/contigs/**
+  - modules/nf-core/macrel/contigs/**
+  - tests/modules/nf-core/macrel/contigs/**
 
 macs2/callpeak:
-- modules/nf-core/macs2/callpeak/**
-- tests/modules/nf-core/macs2/callpeak/**
+  - modules/nf-core/macs2/callpeak/**
+  - tests/modules/nf-core/macs2/callpeak/**
 
 mafft:
-- modules/nf-core/mafft/**
-- tests/modules/nf-core/mafft/**
+  - modules/nf-core/mafft/**
+  - tests/modules/nf-core/mafft/**
 
 mageck/count:
-- modules/nf-core/mageck/count/**
-- tests/modules/nf-core/mageck/count/**
+  - modules/nf-core/mageck/count/**
+  - tests/modules/nf-core/mageck/count/**
 
 mageck/mle:
-- modules/nf-core/mageck/mle/**
-- tests/modules/nf-core/mageck/mle/**
+  - modules/nf-core/mageck/mle/**
+  - tests/modules/nf-core/mageck/mle/**
 
 malt/build:
-- modules/nf-core/malt/build/**
-- tests/modules/nf-core/malt/build_test/**
+  - modules/nf-core/malt/build/**
+  - tests/modules/nf-core/malt/build_test/**
 
 malt/run:
-- modules/nf-core/malt/run/**
-- tests/modules/nf-core/malt/run/**
+  - modules/nf-core/malt/run/**
+  - tests/modules/nf-core/malt/run/**
 
 maltextract:
-- modules/nf-core/maltextract/**
-- tests/modules/nf-core/maltextract/**
+  - modules/nf-core/maltextract/**
+  - tests/modules/nf-core/maltextract/**
 
 manta/convertinversion:
-- modules/nf-core/manta/convertinversion/**
-- tests/modules/nf-core/manta/convertinversion/**
+  - modules/nf-core/manta/convertinversion/**
+  - tests/modules/nf-core/manta/convertinversion/**
 
 manta/germline:
-- modules/nf-core/manta/germline/**
-- tests/modules/nf-core/manta/germline/**
+  - modules/nf-core/manta/germline/**
+  - tests/modules/nf-core/manta/germline/**
 
 manta/somatic:
-- modules/nf-core/manta/somatic/**
-- tests/modules/nf-core/manta/somatic/**
+  - modules/nf-core/manta/somatic/**
+  - tests/modules/nf-core/manta/somatic/**
 
 manta/tumoronly:
-- modules/nf-core/manta/tumoronly/**
-- tests/modules/nf-core/manta/tumoronly/**
+  - modules/nf-core/manta/tumoronly/**
+  - tests/modules/nf-core/manta/tumoronly/**
 
 mapdamage2:
-- modules/nf-core/mapdamage2/**
-- tests/modules/nf-core/mapdamage2/**
+  - modules/nf-core/mapdamage2/**
+  - tests/modules/nf-core/mapdamage2/**
 
 mash/dist:
-- modules/nf-core/mash/dist/**
-- tests/modules/nf-core/mash/dist/**
+  - modules/nf-core/mash/dist/**
+  - tests/modules/nf-core/mash/dist/**
 
 mash/screen:
-- modules/nf-core/mash/screen/**
-- tests/modules/nf-core/mash/screen/**
+  - modules/nf-core/mash/screen/**
+  - tests/modules/nf-core/mash/screen/**
 
 mash/sketch:
-- modules/nf-core/mash/sketch/**
-- tests/modules/nf-core/mash/sketch/**
+  - modules/nf-core/mash/sketch/**
+  - tests/modules/nf-core/mash/sketch/**
 
 mashtree:
-- modules/nf-core/mashtree/**
-- tests/modules/nf-core/mashtree/**
+  - modules/nf-core/mashtree/**
+  - tests/modules/nf-core/mashtree/**
 
 maxbin2:
-- modules/nf-core/maxbin2/**
-- tests/modules/nf-core/maxbin2/**
+  - modules/nf-core/maxbin2/**
+  - tests/modules/nf-core/maxbin2/**
 
 maxquant/lfq:
-- modules/nf-core/maxquant/lfq/**
-- tests/modules/nf-core/maxquant/lfq/**
+  - modules/nf-core/maxquant/lfq/**
+  - tests/modules/nf-core/maxquant/lfq/**
 
 mcroni:
-- modules/nf-core/mcroni/**
-- tests/modules/nf-core/mcroni/**
+  - modules/nf-core/mcroni/**
+  - tests/modules/nf-core/mcroni/**
 
 md5sum:
-- modules/nf-core/md5sum/**
-- tests/modules/nf-core/md5sum/**
+  - modules/nf-core/md5sum/**
+  - tests/modules/nf-core/md5sum/**
 
 medaka:
-- modules/nf-core/medaka/**
-- tests/modules/nf-core/medaka/**
+  - modules/nf-core/medaka/**
+  - tests/modules/nf-core/medaka/**
 
 megahit:
-- modules/nf-core/megahit/**
-- tests/modules/nf-core/megahit/**
+  - modules/nf-core/megahit/**
+  - tests/modules/nf-core/megahit/**
 
 megan/daa2info:
-- modules/nf-core/megan/daa2info/**
-- tests/modules/nf-core/megan/daa2info/**
+  - modules/nf-core/megan/daa2info/**
+  - tests/modules/nf-core/megan/daa2info/**
 
 megan/rma2info:
-- modules/nf-core/megan/rma2info/**
-- tests/modules/nf-core/megan/rma2info/**
+  - modules/nf-core/megan/rma2info/**
+  - tests/modules/nf-core/megan/rma2info/**
 
 meningotype:
-- modules/nf-core/meningotype/**
-- tests/modules/nf-core/meningotype/**
+  - modules/nf-core/meningotype/**
+  - tests/modules/nf-core/meningotype/**
 
 merqury:
-- modules/nf-core/merqury/**
-- tests/modules/nf-core/merqury/**
+  - modules/nf-core/merqury/**
+  - tests/modules/nf-core/merqury/**
 
 merquryfk/katcomp:
-- modules/nf-core/merquryfk/katcomp/**
-- tests/modules/nf-core/merquryfk/katcomp/**
+  - modules/nf-core/merquryfk/katcomp/**
+  - tests/modules/nf-core/merquryfk/katcomp/**
 
 merquryfk/katgc:
-- modules/nf-core/merquryfk/katgc/**
-- tests/modules/nf-core/merquryfk/katgc/**
+  - modules/nf-core/merquryfk/katgc/**
+  - tests/modules/nf-core/merquryfk/katgc/**
 
 merquryfk/merquryfk:
-- modules/nf-core/merquryfk/merquryfk/**
-- tests/modules/nf-core/merquryfk/merquryfk/**
+  - modules/nf-core/merquryfk/merquryfk/**
+  - tests/modules/nf-core/merquryfk/merquryfk/**
 
 merquryfk/ploidyplot:
-- modules/nf-core/merquryfk/ploidyplot/**
-- tests/modules/nf-core/merquryfk/ploidyplot/**
+  - modules/nf-core/merquryfk/ploidyplot/**
+  - tests/modules/nf-core/merquryfk/ploidyplot/**
 
 meryl/count:
-- modules/nf-core/meryl/count/**
-- tests/modules/nf-core/meryl/count/**
+  - modules/nf-core/meryl/count/**
+  - tests/modules/nf-core/meryl/count/**
 
 meryl/histogram:
-- modules/nf-core/meryl/histogram/**
-- tests/modules/nf-core/meryl/histogram/**
+  - modules/nf-core/meryl/histogram/**
+  - tests/modules/nf-core/meryl/histogram/**
 
 meryl/unionsum:
-- modules/nf-core/meryl/unionsum/**
-- tests/modules/nf-core/meryl/unionsum/**
+  - modules/nf-core/meryl/unionsum/**
+  - tests/modules/nf-core/meryl/unionsum/**
 
 metabat2/jgisummarizebamcontigdepths:
-- modules/nf-core/metabat2/jgisummarizebamcontigdepths/**
-- tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/**
+  - modules/nf-core/metabat2/jgisummarizebamcontigdepths/**
+  - tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/**
 
 metabat2/metabat2:
-- modules/nf-core/metabat2/metabat2/**
-- tests/modules/nf-core/metabat2/metabat2/**
+  - modules/nf-core/metabat2/metabat2/**
+  - tests/modules/nf-core/metabat2/metabat2/**
 
 metaphlan3/mergemetaphlantables:
-- modules/nf-core/metaphlan3/mergemetaphlantables/**
-- tests/modules/nf-core/metaphlan3/mergemetaphlantables/**
+  - modules/nf-core/metaphlan3/mergemetaphlantables/**
+  - tests/modules/nf-core/metaphlan3/mergemetaphlantables/**
 
 metaphlan3/metaphlan3:
-- modules/nf-core/metaphlan3/metaphlan3/**
-- tests/modules/nf-core/metaphlan3/metaphlan3/**
+  - modules/nf-core/metaphlan3/metaphlan3/**
+  - tests/modules/nf-core/metaphlan3/metaphlan3/**
 
 methyldackel/extract:
-- modules/nf-core/methyldackel/extract/**
-- tests/modules/nf-core/methyldackel/extract/**
+  - modules/nf-core/methyldackel/extract/**
+  - tests/modules/nf-core/methyldackel/extract/**
 
 methyldackel/mbias:
-- modules/nf-core/methyldackel/mbias/**
-- tests/modules/nf-core/methyldackel/mbias/**
+  - modules/nf-core/methyldackel/mbias/**
+  - tests/modules/nf-core/methyldackel/mbias/**
 
 minia:
-- modules/nf-core/minia/**
-- tests/modules/nf-core/minia/**
+  - modules/nf-core/minia/**
+  - tests/modules/nf-core/minia/**
 
 miniasm:
-- modules/nf-core/miniasm/**
-- tests/modules/nf-core/miniasm/**
+  - modules/nf-core/miniasm/**
+  - tests/modules/nf-core/miniasm/**
 
 minimap2/align:
-- modules/nf-core/minimap2/align/**
-- tests/modules/nf-core/minimap2/align/**
+  - modules/nf-core/minimap2/align/**
+  - tests/modules/nf-core/minimap2/align/**
 
 minimap2/index:
-- modules/nf-core/minimap2/index/**
-- tests/modules/nf-core/minimap2/index/**
+  - modules/nf-core/minimap2/index/**
+  - tests/modules/nf-core/minimap2/index/**
 
 miranda:
-- modules/nf-core/miranda/**
-- tests/modules/nf-core/miranda/**
+  - modules/nf-core/miranda/**
+  - tests/modules/nf-core/miranda/**
 
 mlst:
-- modules/nf-core/mlst/**
-- tests/modules/nf-core/mlst/**
+  - modules/nf-core/mlst/**
+  - tests/modules/nf-core/mlst/**
 
 mobsuite/recon:
-- modules/nf-core/mobsuite/recon/**
-- tests/modules/nf-core/mobsuite/recon/**
+  - modules/nf-core/mobsuite/recon/**
+  - tests/modules/nf-core/mobsuite/recon/**
 
 mosdepth:
-- modules/nf-core/mosdepth/**
-- tests/modules/nf-core/mosdepth/**
+  - modules/nf-core/mosdepth/**
+  - tests/modules/nf-core/mosdepth/**
 
 motus/downloaddb:
-- modules/nf-core/motus/downloaddb/**
-- tests/modules/nf-core/motus/downloaddb/**
+  - modules/nf-core/motus/downloaddb/**
+  - tests/modules/nf-core/motus/downloaddb/**
 
 motus/merge:
-- modules/nf-core/motus/merge/**
-- tests/modules/nf-core/motus/merge/**
+  - modules/nf-core/motus/merge/**
+  - tests/modules/nf-core/motus/merge/**
 
 motus/profile:
-- modules/nf-core/motus/profile/**
-- tests/modules/nf-core/motus/profile/**
+  - modules/nf-core/motus/profile/**
+  - tests/modules/nf-core/motus/profile/**
 
 msisensor/msi:
-- modules/nf-core/msisensor/msi/**
-- tests/modules/nf-core/msisensor/msi/**
+  - modules/nf-core/msisensor/msi/**
+  - tests/modules/nf-core/msisensor/msi/**
 
 msisensor/scan:
-- modules/nf-core/msisensor/scan/**
-- tests/modules/nf-core/msisensor/scan/**
+  - modules/nf-core/msisensor/scan/**
+  - tests/modules/nf-core/msisensor/scan/**
 
 msisensor2/msi:
-- modules/nf-core/msisensor2/msi/**
-- tests/modules/nf-core/msisensor2/msi/**
+  - modules/nf-core/msisensor2/msi/**
+  - tests/modules/nf-core/msisensor2/msi/**
 
 msisensor2/scan:
-- modules/nf-core/msisensor2/scan/**
-- tests/modules/nf-core/msisensor2/scan/**
+  - modules/nf-core/msisensor2/scan/**
+  - tests/modules/nf-core/msisensor2/scan/**
 
 msisensorpro/msi_somatic:
-- modules/nf-core/msisensorpro/msi_somatic/**
-- tests/modules/nf-core/msisensorpro/msi_somatic/**
+  - modules/nf-core/msisensorpro/msi_somatic/**
+  - tests/modules/nf-core/msisensorpro/msi_somatic/**
 
 msisensorpro/scan:
-- modules/nf-core/msisensorpro/scan/**
-- tests/modules/nf-core/msisensorpro/scan/**
+  - modules/nf-core/msisensorpro/scan/**
+  - tests/modules/nf-core/msisensorpro/scan/**
 
 mtnucratio:
-- modules/nf-core/mtnucratio/**
-- tests/modules/nf-core/mtnucratio/**
+  - modules/nf-core/mtnucratio/**
+  - tests/modules/nf-core/mtnucratio/**
 
 multiqc:
-- modules/nf-core/fastqc/**
-- modules/nf-core/multiqc/**
-- tests/modules/nf-core/multiqc/**
+  - modules/nf-core/fastqc/**
+  - modules/nf-core/multiqc/**
+  - tests/modules/nf-core/multiqc/**
 
 multivcfanalyzer:
-- modules/nf-core/multivcfanalyzer/**
-- tests/modules/nf-core/multivcfanalyzer/**
+  - modules/nf-core/multivcfanalyzer/**
+  - tests/modules/nf-core/multivcfanalyzer/**
 
 mummer:
-- modules/nf-core/mummer/**
-- tests/modules/nf-core/mummer/**
+  - modules/nf-core/mummer/**
+  - tests/modules/nf-core/mummer/**
 
 muscle:
-- modules/nf-core/muscle/**
-- tests/modules/nf-core/muscle/**
+  - modules/nf-core/muscle/**
+  - tests/modules/nf-core/muscle/**
 
 mykrobe/predict:
-- modules/nf-core/mykrobe/predict/**
-- tests/modules/nf-core/mykrobe/predict/**
+  - modules/nf-core/mykrobe/predict/**
+  - tests/modules/nf-core/mykrobe/predict/**
 
 nanolyse:
-- modules/nf-core/nanolyse/**
-- tests/modules/nf-core/nanolyse/**
+  - modules/nf-core/nanolyse/**
+  - tests/modules/nf-core/nanolyse/**
 
 nanomonsv/parse:
-- modules/nf-core/nanomonsv/parse/**
-- tests/modules/nf-core/nanomonsv/parse/**
+  - modules/nf-core/nanomonsv/parse/**
+  - tests/modules/nf-core/nanomonsv/parse/**
 
 nanoplot:
-- modules/nf-core/nanoplot/**
-- tests/modules/nf-core/nanoplot/**
+  - modules/nf-core/nanoplot/**
+  - tests/modules/nf-core/nanoplot/**
 
 ncbigenomedownload:
-- modules/nf-core/ncbigenomedownload/**
-- tests/modules/nf-core/ncbigenomedownload/**
+  - modules/nf-core/ncbigenomedownload/**
+  - tests/modules/nf-core/ncbigenomedownload/**
 
 nextclade/datasetget:
-- modules/nf-core/nextclade/datasetget/**
-- tests/modules/nf-core/nextclade/datasetget/**
+  - modules/nf-core/nextclade/datasetget/**
+  - tests/modules/nf-core/nextclade/datasetget/**
 
 nextclade/run:
-- modules/nf-core/nextclade/run/**
-- tests/modules/nf-core/nextclade/run/**
+  - modules/nf-core/nextclade/run/**
+  - tests/modules/nf-core/nextclade/run/**
 
 nextgenmap:
-- modules/nf-core/nextgenmap/**
-- tests/modules/nf-core/nextgenmap/**
+  - modules/nf-core/nextgenmap/**
+  - tests/modules/nf-core/nextgenmap/**
 
 ngmaster:
-- modules/nf-core/ngmaster/**
-- tests/modules/nf-core/ngmaster/**
+  - modules/nf-core/ngmaster/**
+  - tests/modules/nf-core/ngmaster/**
 
 ngscheckmate/ncm:
-- modules/nf-core/ngscheckmate/ncm/**
-- tests/modules/nf-core/ngscheckmate/ncm/**
+  - modules/nf-core/ngscheckmate/ncm/**
+  - tests/modules/nf-core/ngscheckmate/ncm/**
 
 nucmer:
-- modules/nf-core/nucmer/**
-- tests/modules/nf-core/nucmer/**
+  - modules/nf-core/nucmer/**
+  - tests/modules/nf-core/nucmer/**
 
 odgi/build:
-- modules/nf-core/odgi/build/**
-- tests/modules/nf-core/odgi/build_test/**
+  - modules/nf-core/odgi/build/**
+  - tests/modules/nf-core/odgi/build_test/**
 
 odgi/draw:
-- modules/nf-core/odgi/draw/**
-- tests/modules/nf-core/odgi/draw/**
+  - modules/nf-core/odgi/draw/**
+  - tests/modules/nf-core/odgi/draw/**
 
 odgi/layout:
-- modules/nf-core/odgi/layout/**
-- tests/modules/nf-core/odgi/layout/**
+  - modules/nf-core/odgi/layout/**
+  - tests/modules/nf-core/odgi/layout/**
 
 odgi/sort:
-- modules/nf-core/odgi/sort/**
-- tests/modules/nf-core/odgi/sort/**
+  - modules/nf-core/odgi/sort/**
+  - tests/modules/nf-core/odgi/sort/**
 
 odgi/stats:
-- modules/nf-core/odgi/stats/**
-- tests/modules/nf-core/odgi/stats/**
+  - modules/nf-core/odgi/stats/**
+  - tests/modules/nf-core/odgi/stats/**
 
 odgi/unchop:
-- modules/nf-core/odgi/unchop/**
-- tests/modules/nf-core/odgi/unchop/**
+  - modules/nf-core/odgi/unchop/**
+  - tests/modules/nf-core/odgi/unchop/**
 
 odgi/view:
-- modules/nf-core/odgi/view/**
-- tests/modules/nf-core/odgi/view/**
+  - modules/nf-core/odgi/view/**
+  - tests/modules/nf-core/odgi/view/**
 
 odgi/viz:
-- modules/nf-core/odgi/viz/**
-- tests/modules/nf-core/odgi/viz/**
+  - modules/nf-core/odgi/viz/**
+  - tests/modules/nf-core/odgi/viz/**
 
 optitype:
-- modules/nf-core/optitype/**
-- tests/modules/nf-core/optitype/**
+  - modules/nf-core/optitype/**
+  - tests/modules/nf-core/optitype/**
 
 pairix:
-- modules/nf-core/pairix/**
-- tests/modules/nf-core/pairix/**
+  - modules/nf-core/pairix/**
+  - tests/modules/nf-core/pairix/**
 
 pairtools/dedup:
-- modules/nf-core/pairtools/dedup/**
-- tests/modules/nf-core/pairtools/dedup/**
+  - modules/nf-core/pairtools/dedup/**
+  - tests/modules/nf-core/pairtools/dedup/**
 
 pairtools/flip:
-- modules/nf-core/pairtools/flip/**
-- tests/modules/nf-core/pairtools/flip/**
+  - modules/nf-core/pairtools/flip/**
+  - tests/modules/nf-core/pairtools/flip/**
 
 pairtools/parse:
-- modules/nf-core/pairtools/parse/**
-- tests/modules/nf-core/pairtools/parse/**
+  - modules/nf-core/pairtools/parse/**
+  - tests/modules/nf-core/pairtools/parse/**
 
 pairtools/restrict:
-- modules/nf-core/pairtools/restrict/**
-- tests/modules/nf-core/pairtools/restrict/**
+  - modules/nf-core/pairtools/restrict/**
+  - tests/modules/nf-core/pairtools/restrict/**
 
 pairtools/select:
-- modules/nf-core/pairtools/select/**
-- tests/modules/nf-core/pairtools/select/**
+  - modules/nf-core/pairtools/select/**
+  - tests/modules/nf-core/pairtools/select/**
 
 pairtools/sort:
-- modules/nf-core/pairtools/sort/**
-- tests/modules/nf-core/pairtools/sort/**
+  - modules/nf-core/pairtools/sort/**
+  - tests/modules/nf-core/pairtools/sort/**
 
 panaroo/run:
-- modules/nf-core/panaroo/run/**
-- tests/modules/nf-core/panaroo/run/**
+  - modules/nf-core/panaroo/run/**
+  - tests/modules/nf-core/panaroo/run/**
 
 pangolin:
-- modules/nf-core/pangolin/**
-- tests/modules/nf-core/pangolin/**
+  - modules/nf-core/pangolin/**
+  - tests/modules/nf-core/pangolin/**
 
 paraclu:
-- modules/nf-core/paraclu/**
-- tests/modules/nf-core/paraclu/**
+  - modules/nf-core/paraclu/**
+  - tests/modules/nf-core/paraclu/**
 
 pasty:
-- modules/nf-core/pasty/**
-- tests/modules/nf-core/pasty/**
+  - modules/nf-core/pasty/**
+  - tests/modules/nf-core/pasty/**
 
 pbbam/pbmerge:
-- modules/nf-core/pbbam/pbmerge/**
-- tests/modules/nf-core/pbbam/pbmerge/**
+  - modules/nf-core/pbbam/pbmerge/**
+  - tests/modules/nf-core/pbbam/pbmerge/**
 
 pbccs:
-- modules/nf-core/pbccs/**
-- tests/modules/nf-core/pbccs/**
+  - modules/nf-core/pbccs/**
+  - tests/modules/nf-core/pbccs/**
 
 pbptyper:
-- modules/nf-core/pbptyper/**
-- tests/modules/nf-core/pbptyper/**
+  - modules/nf-core/pbptyper/**
+  - tests/modules/nf-core/pbptyper/**
 
 pear:
-- modules/nf-core/pear/**
-- tests/modules/nf-core/pear/**
+  - modules/nf-core/pear/**
+  - tests/modules/nf-core/pear/**
 
 peddy:
-- modules/nf-core/peddy/**
-- tests/modules/nf-core/peddy/**
+  - modules/nf-core/peddy/**
+  - tests/modules/nf-core/peddy/**
 
 phantompeakqualtools:
-- modules/nf-core/phantompeakqualtools/**
-- tests/modules/nf-core/phantompeakqualtools/**
+  - modules/nf-core/phantompeakqualtools/**
+  - tests/modules/nf-core/phantompeakqualtools/**
 
 phyloflash:
-- modules/nf-core/phyloflash/**
-- tests/modules/nf-core/phyloflash/**
+  - modules/nf-core/phyloflash/**
+  - tests/modules/nf-core/phyloflash/**
 
 picard/addorreplacereadgroups:
-- modules/nf-core/picard/addorreplacereadgroups/**
-- tests/modules/nf-core/picard/addorreplacereadgroups/**
+  - modules/nf-core/picard/addorreplacereadgroups/**
+  - tests/modules/nf-core/picard/addorreplacereadgroups/**
 
 picard/cleansam:
-- modules/nf-core/picard/cleansam/**
-- tests/modules/nf-core/picard/cleansam/**
+  - modules/nf-core/picard/cleansam/**
+  - tests/modules/nf-core/picard/cleansam/**
 
 picard/collecthsmetrics:
-- modules/nf-core/picard/collecthsmetrics/**
-- tests/modules/nf-core/picard/collecthsmetrics/**
+  - modules/nf-core/picard/collecthsmetrics/**
+  - tests/modules/nf-core/picard/collecthsmetrics/**
 
 picard/collectmultiplemetrics:
-- modules/nf-core/picard/collectmultiplemetrics/**
-- tests/modules/nf-core/picard/collectmultiplemetrics/**
+  - modules/nf-core/picard/collectmultiplemetrics/**
+  - tests/modules/nf-core/picard/collectmultiplemetrics/**
 
 picard/collectwgsmetrics:
-- modules/nf-core/picard/collectwgsmetrics/**
-- tests/modules/nf-core/picard/collectwgsmetrics/**
+  - modules/nf-core/picard/collectwgsmetrics/**
+  - tests/modules/nf-core/picard/collectwgsmetrics/**
 
 picard/createsequencedictionary:
-- modules/nf-core/picard/createsequencedictionary/**
-- tests/modules/nf-core/picard/createsequencedictionary/**
+  - modules/nf-core/picard/createsequencedictionary/**
+  - tests/modules/nf-core/picard/createsequencedictionary/**
 
 picard/crosscheckfingerprints:
-- modules/nf-core/picard/crosscheckfingerprints/**
-- tests/modules/nf-core/picard/crosscheckfingerprints/**
+  - modules/nf-core/picard/crosscheckfingerprints/**
+  - tests/modules/nf-core/picard/crosscheckfingerprints/**
 
 picard/fastqtosam:
-- modules/nf-core/picard/fastqtosam/**
-- tests/modules/nf-core/picard/fastqtosam/**
+  - modules/nf-core/picard/fastqtosam/**
+  - tests/modules/nf-core/picard/fastqtosam/**
 
 picard/filtersamreads:
-- modules/nf-core/picard/filtersamreads/**
-- tests/modules/nf-core/picard/filtersamreads/**
+  - modules/nf-core/picard/filtersamreads/**
+  - tests/modules/nf-core/picard/filtersamreads/**
 
 picard/fixmateinformation:
-- modules/nf-core/picard/fixmateinformation/**
-- tests/modules/nf-core/picard/fixmateinformation/**
+  - modules/nf-core/picard/fixmateinformation/**
+  - tests/modules/nf-core/picard/fixmateinformation/**
 
 picard/liftovervcf:
-- modules/nf-core/picard/liftovervcf/**
-- tests/modules/nf-core/picard/liftovervcf/**
+  - modules/nf-core/picard/liftovervcf/**
+  - tests/modules/nf-core/picard/liftovervcf/**
 
 picard/markduplicates:
-- modules/nf-core/picard/markduplicates/**
-- tests/modules/nf-core/picard/markduplicates/**
+  - modules/nf-core/picard/markduplicates/**
+  - tests/modules/nf-core/picard/markduplicates/**
 
 picard/mergesamfiles:
-- modules/nf-core/picard/mergesamfiles/**
-- tests/modules/nf-core/picard/mergesamfiles/**
+  - modules/nf-core/picard/mergesamfiles/**
+  - tests/modules/nf-core/picard/mergesamfiles/**
 
 picard/renamesampleinvcf:
-- modules/nf-core/picard/renamesampleinvcf/**
-- tests/modules/nf-core/picard/renamesampleinvcf/**
+  - modules/nf-core/picard/renamesampleinvcf/**
+  - tests/modules/nf-core/picard/renamesampleinvcf/**
 
 picard/sortsam:
-- modules/nf-core/picard/sortsam/**
-- tests/modules/nf-core/picard/sortsam/**
+  - modules/nf-core/picard/sortsam/**
+  - tests/modules/nf-core/picard/sortsam/**
 
 picard/sortvcf:
-- modules/nf-core/picard/sortvcf/**
-- tests/modules/nf-core/picard/sortvcf/**
+  - modules/nf-core/picard/sortvcf/**
+  - tests/modules/nf-core/picard/sortvcf/**
 
 pints/caller:
-- modules/nf-core/pints/caller/**
-- tests/modules/nf-core/pints/caller/**
+  - modules/nf-core/pints/caller/**
+  - tests/modules/nf-core/pints/caller/**
 
 pirate:
-- modules/nf-core/pirate/**
-- tests/modules/nf-core/pirate/**
+  - modules/nf-core/pirate/**
+  - tests/modules/nf-core/pirate/**
 
 plasmidfinder:
-- modules/nf-core/plasmidfinder/**
-- tests/modules/nf-core/plasmidfinder/**
+  - modules/nf-core/plasmidfinder/**
+  - tests/modules/nf-core/plasmidfinder/**
 
 plasmidid:
-- modules/nf-core/plasmidid/**
-- tests/modules/nf-core/plasmidid/**
+  - modules/nf-core/plasmidid/**
+  - tests/modules/nf-core/plasmidid/**
 
 plink/extract:
-- modules/nf-core/plink/extract/**
-- tests/modules/nf-core/plink/extract/**
+  - modules/nf-core/plink/extract/**
+  - tests/modules/nf-core/plink/extract/**
 
 plink/vcf:
-- modules/nf-core/plink/vcf/**
-- tests/modules/nf-core/plink/vcf/**
+  - modules/nf-core/plink/vcf/**
+  - tests/modules/nf-core/plink/vcf/**
 
 plink2/extract:
-- modules/nf-core/plink2/extract/**
-- tests/modules/nf-core/plink2/extract/**
+  - modules/nf-core/plink2/extract/**
+  - tests/modules/nf-core/plink2/extract/**
 
 plink2/score:
-- modules/nf-core/plink2/score/**
-- tests/modules/nf-core/plink2/score/**
+  - modules/nf-core/plink2/score/**
+  - tests/modules/nf-core/plink2/score/**
 
 plink2/vcf:
-- modules/nf-core/plink2/vcf/**
-- tests/modules/nf-core/plink2/vcf/**
+  - modules/nf-core/plink2/vcf/**
+  - tests/modules/nf-core/plink2/vcf/**
 
 pmdtools/filter:
-- modules/nf-core/pmdtools/filter/**
-- tests/modules/nf-core/pmdtools/filter/**
+  - modules/nf-core/pmdtools/filter/**
+  - tests/modules/nf-core/pmdtools/filter/**
 
 porechop:
-- modules/nf-core/porechop/**
-- tests/modules/nf-core/porechop/**
+  - modules/nf-core/porechop/**
+  - tests/modules/nf-core/porechop/**
 
 preseq/ccurve:
-- modules/nf-core/preseq/ccurve/**
-- tests/modules/nf-core/preseq/ccurve/**
+  - modules/nf-core/preseq/ccurve/**
+  - tests/modules/nf-core/preseq/ccurve/**
 
 preseq/lcextrap:
-- modules/nf-core/preseq/lcextrap/**
-- tests/modules/nf-core/preseq/lcextrap/**
+  - modules/nf-core/preseq/lcextrap/**
+  - tests/modules/nf-core/preseq/lcextrap/**
 
 pretextmap:
-- modules/nf-core/pretextmap/**
-- tests/modules/nf-core/pretextmap/**
+  - modules/nf-core/pretextmap/**
+  - tests/modules/nf-core/pretextmap/**
 
 prinseqplusplus:
-- modules/nf-core/prinseqplusplus/**
-- tests/modules/nf-core/prinseqplusplus/**
+  - modules/nf-core/prinseqplusplus/**
+  - tests/modules/nf-core/prinseqplusplus/**
 
 prodigal:
-- modules/nf-core/prodigal/**
-- tests/modules/nf-core/prodigal/**
+  - modules/nf-core/prodigal/**
+  - tests/modules/nf-core/prodigal/**
 
 prokka:
-- modules/nf-core/prokka/**
-- tests/modules/nf-core/prokka/**
+  - modules/nf-core/prokka/**
+  - tests/modules/nf-core/prokka/**
 
 pycoqc:
-- modules/nf-core/pycoqc/**
-- tests/modules/nf-core/pycoqc/**
+  - modules/nf-core/pycoqc/**
+  - tests/modules/nf-core/pycoqc/**
 
 pydamage/analyze:
-- modules/nf-core/pydamage/analyze/**
-- tests/modules/nf-core/pydamage/analyze/**
+  - modules/nf-core/pydamage/analyze/**
+  - tests/modules/nf-core/pydamage/analyze/**
 
 pydamage/filter:
-- modules/nf-core/pydamage/filter/**
-- tests/modules/nf-core/pydamage/filter/**
+  - modules/nf-core/pydamage/filter/**
+  - tests/modules/nf-core/pydamage/filter/**
 
 qcat:
-- modules/nf-core/qcat/**
-- tests/modules/nf-core/qcat/**
+  - modules/nf-core/qcat/**
+  - tests/modules/nf-core/qcat/**
 
 qualimap/bamqc:
-- modules/nf-core/qualimap/bamqc/**
-- tests/modules/nf-core/qualimap/bamqc/**
+  - modules/nf-core/qualimap/bamqc/**
+  - tests/modules/nf-core/qualimap/bamqc/**
 
 qualimap/bamqccram:
-- modules/nf-core/qualimap/bamqccram/**
-- tests/modules/nf-core/qualimap/bamqccram/**
+  - modules/nf-core/qualimap/bamqccram/**
+  - tests/modules/nf-core/qualimap/bamqccram/**
 
 quast:
-- modules/nf-core/quast/**
-- tests/modules/nf-core/quast/**
+  - modules/nf-core/quast/**
+  - tests/modules/nf-core/quast/**
 
 racon:
-- modules/nf-core/racon/**
-- tests/modules/nf-core/racon/**
+  - modules/nf-core/racon/**
+  - tests/modules/nf-core/racon/**
 
 rapidnj:
-- modules/nf-core/rapidnj/**
-- tests/modules/nf-core/rapidnj/**
+  - modules/nf-core/rapidnj/**
+  - tests/modules/nf-core/rapidnj/**
 
 rasusa:
-- modules/nf-core/rasusa/**
-- tests/modules/nf-core/rasusa/**
+  - modules/nf-core/rasusa/**
+  - tests/modules/nf-core/rasusa/**
 
 raven:
-- modules/nf-core/raven/**
-- tests/modules/nf-core/raven/**
+  - modules/nf-core/raven/**
+  - tests/modules/nf-core/raven/**
 
 raxmlng:
-- modules/nf-core/raxmlng/**
-- tests/modules/nf-core/raxmlng/**
+  - modules/nf-core/raxmlng/**
+  - tests/modules/nf-core/raxmlng/**
 
 rgi/main:
-- modules/nf-core/rgi/main/**
-- tests/modules/nf-core/rgi/main/**
+  - modules/nf-core/rgi/main/**
+  - tests/modules/nf-core/rgi/main/**
 
 rhocall/annotate:
-- modules/nf-core/rhocall/annotate/**
-- tests/modules/nf-core/rhocall/annotate/**
+  - modules/nf-core/rhocall/annotate/**
+  - tests/modules/nf-core/rhocall/annotate/**
 
 rmarkdownnotebook:
-- modules/nf-core/rmarkdownnotebook/**
-- tests/modules/nf-core/rmarkdownnotebook/**
+  - modules/nf-core/rmarkdownnotebook/**
+  - tests/modules/nf-core/rmarkdownnotebook/**
 
 roary:
-- modules/nf-core/roary/**
-- tests/modules/nf-core/roary/**
+  - modules/nf-core/roary/**
+  - tests/modules/nf-core/roary/**
 
 rsem/calculateexpression:
-- modules/nf-core/rsem/calculateexpression/**
-- tests/modules/nf-core/rsem/calculateexpression/**
+  - modules/nf-core/rsem/calculateexpression/**
+  - tests/modules/nf-core/rsem/calculateexpression/**
 
 rsem/preparereference:
-- modules/nf-core/rsem/preparereference/**
-- tests/modules/nf-core/rsem/preparereference/**
+  - modules/nf-core/rsem/preparereference/**
+  - tests/modules/nf-core/rsem/preparereference/**
 
 rseqc/bamstat:
-- modules/nf-core/rseqc/bamstat/**
-- tests/modules/nf-core/rseqc/bamstat/**
+  - modules/nf-core/rseqc/bamstat/**
+  - tests/modules/nf-core/rseqc/bamstat/**
 
 rseqc/inferexperiment:
-- modules/nf-core/rseqc/inferexperiment/**
-- tests/modules/nf-core/rseqc/inferexperiment/**
+  - modules/nf-core/rseqc/inferexperiment/**
+  - tests/modules/nf-core/rseqc/inferexperiment/**
 
 rseqc/innerdistance:
-- modules/nf-core/rseqc/innerdistance/**
-- tests/modules/nf-core/rseqc/innerdistance/**
+  - modules/nf-core/rseqc/innerdistance/**
+  - tests/modules/nf-core/rseqc/innerdistance/**
 
 rseqc/junctionannotation:
-- modules/nf-core/rseqc/junctionannotation/**
-- tests/modules/nf-core/rseqc/junctionannotation/**
+  - modules/nf-core/rseqc/junctionannotation/**
+  - tests/modules/nf-core/rseqc/junctionannotation/**
 
 rseqc/junctionsaturation:
-- modules/nf-core/rseqc/junctionsaturation/**
-- tests/modules/nf-core/rseqc/junctionsaturation/**
+  - modules/nf-core/rseqc/junctionsaturation/**
+  - tests/modules/nf-core/rseqc/junctionsaturation/**
 
 rseqc/readdistribution:
-- modules/nf-core/rseqc/readdistribution/**
-- tests/modules/nf-core/rseqc/readdistribution/**
+  - modules/nf-core/rseqc/readdistribution/**
+  - tests/modules/nf-core/rseqc/readdistribution/**
 
 rseqc/readduplication:
-- modules/nf-core/rseqc/readduplication/**
-- tests/modules/nf-core/rseqc/readduplication/**
+  - modules/nf-core/rseqc/readduplication/**
+  - tests/modules/nf-core/rseqc/readduplication/**
 
 rseqc/tin:
-- modules/nf-core/rseqc/tin/**
-- tests/modules/nf-core/rseqc/tin/**
+  - modules/nf-core/rseqc/tin/**
+  - tests/modules/nf-core/rseqc/tin/**
 
 rtgtools/pedfilter:
-- modules/nf-core/rtgtools/pedfilter/**
-- tests/modules/nf-core/rtgtools/pedfilter/**
+  - modules/nf-core/rtgtools/pedfilter/**
+  - tests/modules/nf-core/rtgtools/pedfilter/**
 
 rtgtools/vcfeval:
-- modules/nf-core/rtgtools/vcfeval/**
-- tests/modules/nf-core/rtgtools/vcfeval/**
+  - modules/nf-core/rtgtools/vcfeval/**
+  - tests/modules/nf-core/rtgtools/vcfeval/**
 
 salmon/index:
-- modules/nf-core/salmon/index/**
-- tests/modules/nf-core/salmon/index/**
+  - modules/nf-core/salmon/index/**
+  - tests/modules/nf-core/salmon/index/**
 
 salmon/quant:
-- modules/nf-core/salmon/quant/**
-- tests/modules/nf-core/salmon/quant/**
+  - modules/nf-core/salmon/quant/**
+  - tests/modules/nf-core/salmon/quant/**
 
 samblaster:
-- modules/nf-core/samblaster/**
-- tests/modules/nf-core/samblaster/**
+  - modules/nf-core/samblaster/**
+  - tests/modules/nf-core/samblaster/**
 
 samtools/ampliconclip:
-- modules/nf-core/samtools/ampliconclip/**
-- tests/modules/nf-core/samtools/ampliconclip/**
+  - modules/nf-core/samtools/ampliconclip/**
+  - tests/modules/nf-core/samtools/ampliconclip/**
 
 samtools/bam2fq:
-- modules/nf-core/samtools/bam2fq/**
-- tests/modules/nf-core/samtools/bam2fq/**
+  - modules/nf-core/samtools/bam2fq/**
+  - tests/modules/nf-core/samtools/bam2fq/**
 
 samtools/calmd:
-- modules/nf-core/samtools/calmd/**
-- tests/modules/nf-core/samtools/calmd/**
+  - modules/nf-core/samtools/calmd/**
+  - tests/modules/nf-core/samtools/calmd/**
 
 samtools/collate:
-- modules/nf-core/samtools/collate/**
-- tests/modules/nf-core/samtools/collate/**
+  - modules/nf-core/samtools/collate/**
+  - tests/modules/nf-core/samtools/collate/**
 
 samtools/collatefastq:
-- modules/nf-core/samtools/collatefastq/**
-- tests/modules/nf-core/samtools/collatefastq/**
+  - modules/nf-core/samtools/collatefastq/**
+  - tests/modules/nf-core/samtools/collatefastq/**
 
 samtools/convert:
-- modules/nf-core/samtools/convert/**
-- tests/modules/nf-core/samtools/convert/**
+  - modules/nf-core/samtools/convert/**
+  - tests/modules/nf-core/samtools/convert/**
 
 samtools/depth:
-- modules/nf-core/samtools/depth/**
-- tests/modules/nf-core/samtools/depth/**
+  - modules/nf-core/samtools/depth/**
+  - tests/modules/nf-core/samtools/depth/**
 
 samtools/dict:
-- modules/nf-core/samtools/dict/**
-- tests/modules/nf-core/samtools/dict/**
+  - modules/nf-core/samtools/dict/**
+  - tests/modules/nf-core/samtools/dict/**
 
 samtools/faidx:
-- modules/nf-core/samtools/faidx/**
-- tests/modules/nf-core/samtools/faidx/**
+  - modules/nf-core/samtools/faidx/**
+  - tests/modules/nf-core/samtools/faidx/**
 
 samtools/fasta:
-- modules/nf-core/samtools/fasta/**
-- tests/modules/nf-core/samtools/fasta/**
+  - modules/nf-core/samtools/fasta/**
+  - tests/modules/nf-core/samtools/fasta/**
 
 samtools/fastq:
-- modules/nf-core/samtools/fastq/**
-- tests/modules/nf-core/samtools/fastq/**
+  - modules/nf-core/samtools/fastq/**
+  - tests/modules/nf-core/samtools/fastq/**
 
 samtools/fixmate:
-- modules/nf-core/samtools/fixmate/**
-- tests/modules/nf-core/samtools/fixmate/**
+  - modules/nf-core/samtools/fixmate/**
+  - tests/modules/nf-core/samtools/fixmate/**
 
 samtools/flagstat:
-- modules/nf-core/samtools/flagstat/**
-- tests/modules/nf-core/samtools/flagstat/**
+  - modules/nf-core/samtools/flagstat/**
+  - tests/modules/nf-core/samtools/flagstat/**
 
 samtools/getrg:
-- modules/nf-core/samtools/getrg/**
-- tests/modules/nf-core/samtools/getrg/**
+  - modules/nf-core/samtools/getrg/**
+  - tests/modules/nf-core/samtools/getrg/**
 
 samtools/idxstats:
-- modules/nf-core/samtools/idxstats/**
-- tests/modules/nf-core/samtools/idxstats/**
+  - modules/nf-core/samtools/idxstats/**
+  - tests/modules/nf-core/samtools/idxstats/**
 
 samtools/index:
-- modules/nf-core/samtools/index/**
-- tests/modules/nf-core/samtools/index/**
+  - modules/nf-core/samtools/index/**
+  - tests/modules/nf-core/samtools/index/**
 
 samtools/markdup:
-- modules/nf-core/samtools/markdup/**
-- tests/modules/nf-core/samtools/markdup/**
+  - modules/nf-core/samtools/markdup/**
+  - tests/modules/nf-core/samtools/markdup/**
 
 samtools/merge:
-- modules/nf-core/samtools/merge/**
-- tests/modules/nf-core/samtools/merge/**
+  - modules/nf-core/samtools/merge/**
+  - tests/modules/nf-core/samtools/merge/**
 
 samtools/mpileup:
-- modules/nf-core/samtools/mpileup/**
-- tests/modules/nf-core/samtools/mpileup/**
+  - modules/nf-core/samtools/mpileup/**
+  - tests/modules/nf-core/samtools/mpileup/**
 
 samtools/sort:
-- modules/nf-core/samtools/sort/**
-- tests/modules/nf-core/samtools/sort/**
+  - modules/nf-core/samtools/sort/**
+  - tests/modules/nf-core/samtools/sort/**
 
 samtools/stats:
-- modules/nf-core/samtools/stats/**
-- tests/modules/nf-core/samtools/stats/**
+  - modules/nf-core/samtools/stats/**
+  - tests/modules/nf-core/samtools/stats/**
 
 samtools/view:
-- modules/nf-core/samtools/view/**
-- tests/modules/nf-core/samtools/view/**
+  - modules/nf-core/samtools/view/**
+  - tests/modules/nf-core/samtools/view/**
 
 scoary:
-- modules/nf-core/scoary/**
-- tests/modules/nf-core/scoary/**
+  - modules/nf-core/scoary/**
+  - tests/modules/nf-core/scoary/**
 
 scramble/clusteranalysis:
-- modules/nf-core/scramble/clusteranalysis/**
-- tests/modules/nf-core/scramble/clusteranalysis/**
+  - modules/nf-core/scramble/clusteranalysis/**
+  - tests/modules/nf-core/scramble/clusteranalysis/**
 
 scramble/clusteridentifier:
-- modules/nf-core/scramble/clusteridentifier/**
-- tests/modules/nf-core/scramble/clusteridentifier/**
+  - modules/nf-core/scramble/clusteridentifier/**
+  - tests/modules/nf-core/scramble/clusteridentifier/**
 
 seacr/callpeak:
-- modules/nf-core/seacr/callpeak/**
-- tests/modules/nf-core/seacr/callpeak/**
+  - modules/nf-core/seacr/callpeak/**
+  - tests/modules/nf-core/seacr/callpeak/**
 
 segemehl/align:
-- modules/nf-core/segemehl/align/**
-- tests/modules/nf-core/segemehl/align/**
+  - modules/nf-core/segemehl/align/**
+  - tests/modules/nf-core/segemehl/align/**
 
 segemehl/index:
-- modules/nf-core/segemehl/index/**
-- tests/modules/nf-core/segemehl/index/**
+  - modules/nf-core/segemehl/index/**
+  - tests/modules/nf-core/segemehl/index/**
 
 seqkit/pair:
-- modules/nf-core/seqkit/pair/**
-- tests/modules/nf-core/seqkit/pair/**
+  - modules/nf-core/seqkit/pair/**
+  - tests/modules/nf-core/seqkit/pair/**
 
 seqkit/replace:
-- modules/nf-core/seqkit/replace/**
-- tests/modules/nf-core/seqkit/replace/**
+  - modules/nf-core/seqkit/replace/**
+  - tests/modules/nf-core/seqkit/replace/**
 
 seqkit/split2:
-- modules/nf-core/seqkit/split2/**
-- tests/modules/nf-core/seqkit/split2/**
+  - modules/nf-core/seqkit/split2/**
+  - tests/modules/nf-core/seqkit/split2/**
 
 seqkit/stats:
-- modules/nf-core/seqkit/stats/**
-- tests/modules/nf-core/seqkit/stats/**
+  - modules/nf-core/seqkit/stats/**
+  - tests/modules/nf-core/seqkit/stats/**
 
 seqsero2:
-- modules/nf-core/seqsero2/**
-- tests/modules/nf-core/seqsero2/**
+  - modules/nf-core/seqsero2/**
+  - tests/modules/nf-core/seqsero2/**
 
 seqtk/mergepe:
-- modules/nf-core/seqtk/mergepe/**
-- tests/modules/nf-core/seqtk/mergepe/**
+  - modules/nf-core/seqtk/mergepe/**
+  - tests/modules/nf-core/seqtk/mergepe/**
 
 seqtk/rename:
-- modules/nf-core/seqtk/rename/**
-- tests/modules/nf-core/seqtk/rename/**
+  - modules/nf-core/seqtk/rename/**
+  - tests/modules/nf-core/seqtk/rename/**
 
 seqtk/sample:
-- modules/nf-core/seqtk/sample/**
-- tests/modules/nf-core/seqtk/sample/**
+  - modules/nf-core/seqtk/sample/**
+  - tests/modules/nf-core/seqtk/sample/**
 
 seqtk/seq:
-- modules/nf-core/seqtk/seq/**
-- tests/modules/nf-core/seqtk/seq/**
+  - modules/nf-core/seqtk/seq/**
+  - tests/modules/nf-core/seqtk/seq/**
 
 seqtk/subseq:
-- modules/nf-core/seqtk/subseq/**
-- tests/modules/nf-core/seqtk/subseq/**
+  - modules/nf-core/seqtk/subseq/**
+  - tests/modules/nf-core/seqtk/subseq/**
 
 sequenzautils/bam2seqz:
-- modules/nf-core/sequenzautils/bam2seqz/**
-- tests/modules/nf-core/sequenzautils/bam2seqz/**
+  - modules/nf-core/sequenzautils/bam2seqz/**
+  - tests/modules/nf-core/sequenzautils/bam2seqz/**
 
 sequenzautils/gcwiggle:
-- modules/nf-core/sequenzautils/gcwiggle/**
-- tests/modules/nf-core/sequenzautils/gcwiggle/**
+  - modules/nf-core/sequenzautils/gcwiggle/**
+  - tests/modules/nf-core/sequenzautils/gcwiggle/**
 
 seqwish/induce:
-- modules/nf-core/seqwish/induce/**
-- tests/modules/nf-core/seqwish/induce/**
+  - modules/nf-core/seqwish/induce/**
+  - tests/modules/nf-core/seqwish/induce/**
 
 seroba/run:
-- modules/nf-core/seroba/run/**
-- tests/modules/nf-core/seroba/run/**
+  - modules/nf-core/seroba/run/**
+  - tests/modules/nf-core/seroba/run/**
 
 sexdeterrmine:
-- modules/nf-core/sexdeterrmine/**
-- tests/modules/nf-core/sexdeterrmine/**
+  - modules/nf-core/sexdeterrmine/**
+  - tests/modules/nf-core/sexdeterrmine/**
 
 shasta:
-- modules/nf-core/shasta/**
-- tests/modules/nf-core/shasta/**
+  - modules/nf-core/shasta/**
+  - tests/modules/nf-core/shasta/**
 
 shasum:
-- modules/nf-core/shasum/**
-- tests/modules/nf-core/shasum/**
+  - modules/nf-core/shasum/**
+  - tests/modules/nf-core/shasum/**
 
 shigatyper:
-- modules/nf-core/shigatyper/**
-- tests/modules/nf-core/shigatyper/**
+  - modules/nf-core/shigatyper/**
+  - tests/modules/nf-core/shigatyper/**
 
 shinyngs/app:
-- modules/nf-core/shinyngs/app/**
-- tests/modules/nf-core/shinyngs/app/**
+  - modules/nf-core/shinyngs/app/**
+  - tests/modules/nf-core/shinyngs/app/**
 
 shinyngs/staticexploratory:
-- modules/nf-core/shinyngs/staticexploratory/**
-- tests/modules/nf-core/shinyngs/staticexploratory/**
+  - modules/nf-core/shinyngs/staticexploratory/**
+  - tests/modules/nf-core/shinyngs/staticexploratory/**
 
 shovill:
-- modules/nf-core/shovill/**
-- tests/modules/nf-core/shovill/**
+  - modules/nf-core/shovill/**
+  - tests/modules/nf-core/shovill/**
 
 sistr:
-- modules/nf-core/sistr/**
-- tests/modules/nf-core/sistr/**
+  - modules/nf-core/sistr/**
+  - tests/modules/nf-core/sistr/**
 
 slimfastq:
-- modules/nf-core/slimfastq/**
-- tests/modules/nf-core/slimfastq/**
+  - modules/nf-core/slimfastq/**
+  - tests/modules/nf-core/slimfastq/**
 
 snapaligner/align:
-- modules/nf-core/snapaligner/align/**
-- tests/modules/nf-core/snapaligner/align/**
+  - modules/nf-core/snapaligner/align/**
+  - tests/modules/nf-core/snapaligner/align/**
 
 snapaligner/index:
-- modules/nf-core/snapaligner/index/**
-- tests/modules/nf-core/snapaligner/index/**
+  - modules/nf-core/snapaligner/index/**
+  - tests/modules/nf-core/snapaligner/index/**
 
 snippy/core:
-- modules/nf-core/snippy/core/**
-- tests/modules/nf-core/snippy/core/**
+  - modules/nf-core/snippy/core/**
+  - tests/modules/nf-core/snippy/core/**
 
 snippy/run:
-- modules/nf-core/snippy/run/**
-- tests/modules/nf-core/snippy/run/**
+  - modules/nf-core/snippy/run/**
+  - tests/modules/nf-core/snippy/run/**
 
 snpdists:
-- modules/nf-core/snpdists/**
-- tests/modules/nf-core/snpdists/**
+  - modules/nf-core/snpdists/**
+  - tests/modules/nf-core/snpdists/**
 
 snpeff:
-- modules/nf-core/snpeff/**
-- tests/modules/nf-core/snpeff/**
+  - modules/nf-core/snpeff/**
+  - tests/modules/nf-core/snpeff/**
 
 snpsift/split:
-- modules/nf-core/snpsift/split/**
-- tests/modules/nf-core/snpsift/split/**
+  - modules/nf-core/snpsift/split/**
+  - tests/modules/nf-core/snpsift/split/**
 
 snpsites:
-- modules/nf-core/snpsites/**
-- tests/modules/nf-core/snpsites/**
+  - modules/nf-core/snpsites/**
+  - tests/modules/nf-core/snpsites/**
 
 somalier/extract:
-- modules/nf-core/somalier/extract/**
-- tests/modules/nf-core/somalier/extract/**
+  - modules/nf-core/somalier/extract/**
+  - tests/modules/nf-core/somalier/extract/**
 
 somalier/relate:
-- modules/nf-core/somalier/relate/**
-- tests/modules/nf-core/somalier/relate/**
+  - modules/nf-core/somalier/relate/**
+  - tests/modules/nf-core/somalier/relate/**
 
 sourmash/gather:
-- modules/nf-core/sourmash/gather/**
-- tests/modules/nf-core/sourmash/gather/**
+  - modules/nf-core/sourmash/gather/**
+  - tests/modules/nf-core/sourmash/gather/**
 
 sourmash/sketch:
-- modules/nf-core/sourmash/sketch/**
-- tests/modules/nf-core/sourmash/sketch/**
+  - modules/nf-core/sourmash/sketch/**
+  - tests/modules/nf-core/sourmash/sketch/**
 
 spades:
-- modules/nf-core/spades/**
-- tests/modules/nf-core/spades/**
+  - modules/nf-core/spades/**
+  - tests/modules/nf-core/spades/**
 
 spatyper:
-- modules/nf-core/spatyper/**
-- tests/modules/nf-core/spatyper/**
+  - modules/nf-core/spatyper/**
+  - tests/modules/nf-core/spatyper/**
 
 sratools/fasterqdump:
-- modules/nf-core/sratools/fasterqdump/**
-- tests/modules/nf-core/sratools/fasterqdump/**
+  - modules/nf-core/sratools/fasterqdump/**
+  - tests/modules/nf-core/sratools/fasterqdump/**
 
 sratools/prefetch:
-- modules/nf-core/sratools/prefetch/**
-- tests/modules/nf-core/sratools/prefetch/**
+  - modules/nf-core/sratools/prefetch/**
+  - tests/modules/nf-core/sratools/prefetch/**
 
 srst2/srst2:
-- modules/nf-core/srst2/srst2/**
-- tests/modules/nf-core/srst2/srst2/**
+  - modules/nf-core/srst2/srst2/**
+  - tests/modules/nf-core/srst2/srst2/**
 
 ssuissero:
-- modules/nf-core/ssuissero/**
-- tests/modules/nf-core/ssuissero/**
+  - modules/nf-core/ssuissero/**
+  - tests/modules/nf-core/ssuissero/**
 
 stadeniolib/scramble:
-- modules/nf-core/stadeniolib/scramble/**
-- tests/modules/nf-core/stadeniolib/scramble/**
+  - modules/nf-core/stadeniolib/scramble/**
+  - tests/modules/nf-core/stadeniolib/scramble/**
 
 staphopiasccmec:
-- modules/nf-core/staphopiasccmec/**
-- tests/modules/nf-core/staphopiasccmec/**
+  - modules/nf-core/staphopiasccmec/**
+  - tests/modules/nf-core/staphopiasccmec/**
 
 star/align:
-- modules/nf-core/star/align/**
-- tests/modules/nf-core/star/align/**
+  - modules/nf-core/star/align/**
+  - tests/modules/nf-core/star/align/**
 
 star/genomegenerate:
-- modules/nf-core/star/genomegenerate/**
-- tests/modules/nf-core/star/genomegenerate/**
+  - modules/nf-core/star/genomegenerate/**
+  - tests/modules/nf-core/star/genomegenerate/**
 
 stranger:
-- modules/nf-core/stranger/**
-- tests/modules/nf-core/stranger/**
+  - modules/nf-core/stranger/**
+  - tests/modules/nf-core/stranger/**
 
 strelka/germline:
-- modules/nf-core/strelka/germline/**
-- tests/modules/nf-core/strelka/germline/**
+  - modules/nf-core/strelka/germline/**
+  - tests/modules/nf-core/strelka/germline/**
 
 strelka/somatic:
-- modules/nf-core/strelka/somatic/**
-- tests/modules/nf-core/strelka/somatic/**
+  - modules/nf-core/strelka/somatic/**
+  - tests/modules/nf-core/strelka/somatic/**
 
 stringtie/merge:
-- modules/nf-core/stringtie/merge/**
-- tests/modules/nf-core/stringtie/merge/**
+  - modules/nf-core/stringtie/merge/**
+  - tests/modules/nf-core/stringtie/merge/**
 
 stringtie/stringtie:
-- modules/nf-core/stringtie/stringtie/**
-- tests/modules/nf-core/stringtie/stringtie/**
+  - modules/nf-core/stringtie/stringtie/**
+  - tests/modules/nf-core/stringtie/stringtie/**
 
 subread/featurecounts:
-- modules/nf-core/subread/featurecounts/**
-- tests/modules/nf-core/subread/featurecounts/**
+  - modules/nf-core/subread/featurecounts/**
+  - tests/modules/nf-core/subread/featurecounts/**
 
 subworkflows/align_bowtie2:
-- subworkflows/nf-core/align_bowtie2/**
-- tests/subworkflows/nf-core/align_bowtie2/**
+  - subworkflows/nf-core/align_bowtie2/**
+  - tests/subworkflows/nf-core/align_bowtie2/**
 
 subworkflows/annotation/ensemblvep:
-- subworkflows/nf-core/annotation/ensemblvep/**
-- tests/subworkflows/nf-core/annotation/ensemblvep/**
+  - subworkflows/nf-core/annotation/ensemblvep/**
+  - tests/subworkflows/nf-core/annotation/ensemblvep/**
 
 subworkflows/annotation/snpeff:
-- subworkflows/nf-core/annotation/snpeff/**
-- tests/subworkflows/nf-core/annotation/snpeff/**
+  - subworkflows/nf-core/annotation/snpeff/**
+  - tests/subworkflows/nf-core/annotation/snpeff/**
 
 subworkflows/bam_dedup_stats_samtools_umitools:
-- subworkflows/nf-core/bam_dedup_stats_samtools_umitools/**
-- tests/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/**
+  - subworkflows/nf-core/bam_dedup_stats_samtools_umitools/**
+  - tests/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/**
 
 subworkflows/bam_markduplicates_picard:
-- subworkflows/nf-core/bam_markduplicates_picard/**
-- tests/subworkflows/nf-core/bam_markduplicates_picard/**
+  - subworkflows/nf-core/bam_markduplicates_picard/**
+  - tests/subworkflows/nf-core/bam_markduplicates_picard/**
 
 subworkflows/bam_qc_picard:
-- subworkflows/nf-core/bam_qc_picard/**
-- tests/subworkflows/nf-core/bam_qc_picard/**
+  - subworkflows/nf-core/bam_qc_picard/**
+  - tests/subworkflows/nf-core/bam_qc_picard/**
 
 subworkflows/bam_rseqc:
-- subworkflows/nf-core/bam_rseqc/**
-- tests/subworkflows/nf-core/bam_rseqc/**
+  - subworkflows/nf-core/bam_rseqc/**
+  - tests/subworkflows/nf-core/bam_rseqc/**
 
 subworkflows/bam_sort_samtools:
-- subworkflows/nf-core/bam_sort_samtools/**
-- tests/subworkflows/nf-core/bam_sort_samtools/**
+  - subworkflows/nf-core/bam_sort_samtools/**
+  - tests/subworkflows/nf-core/bam_sort_samtools/**
 
 subworkflows/bam_sort_stats_samtools:
-- subworkflows/nf-core/bam_sort_stats_samtools/**
-- tests/subworkflows/nf-core/bam_sort_stats_samtools/**
+  - subworkflows/nf-core/bam_sort_stats_samtools/**
+  - tests/subworkflows/nf-core/bam_sort_stats_samtools/**
 
 subworkflows/bam_stats_samtools:
-- subworkflows/nf-core/bam_stats_samtools/**
-- tests/subworkflows/nf-core/bam_stats_samtools/**
+  - subworkflows/nf-core/bam_stats_samtools/**
+  - tests/subworkflows/nf-core/bam_stats_samtools/**
 
 subworkflows/bcl_demultiplex:
-- subworkflows/nf-core/bcl_demultiplex/**
-- tests/subworkflows/nf-core/bcl_demultiplex/**
+  - subworkflows/nf-core/bcl_demultiplex/**
+  - tests/subworkflows/nf-core/bcl_demultiplex/**
 
 subworkflows/bedgraph_bedclip_bedgraphtobigwig:
-- subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/**
-- tests/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/**
+  - subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/**
+  - tests/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/**
 
 subworkflows/fasta_index_dna:
-- subworkflows/nf-core/fasta_index_dna/**
-- tests/subworkflows/nf-core/fasta_index_dna/**
+  - subworkflows/nf-core/fasta_index_dna/**
+  - tests/subworkflows/nf-core/fasta_index_dna/**
 
 subworkflows/fastq_align_dna:
-- subworkflows/nf-core/fastq_align_dna/**
-- tests/subworkflows/nf-core/fastq_align_dna/**
+  - subworkflows/nf-core/fastq_align_dna/**
+  - tests/subworkflows/nf-core/fastq_align_dna/**
 
 subworkflows/fastq_align_hisat2:
-- subworkflows/nf-core/fastq_align_hisat2/**
-- tests/subworkflows/nf-core/fastq_align_hisat2/**
+  - subworkflows/nf-core/fastq_align_hisat2/**
+  - tests/subworkflows/nf-core/fastq_align_hisat2/**
 
 subworkflows/fastq_align_star:
-- subworkflows/nf-core/fastq_align_star/**
-- tests/subworkflows/nf-core/fastq_align_star/**
+  - subworkflows/nf-core/fastq_align_star/**
+  - tests/subworkflows/nf-core/fastq_align_star/**
 
 subworkflows/fastq_contam_seqtk_kraken:
-- subworkflows/nf-core/fastq_contam_seqtk_kraken/**
-- tests/subworkflows/nf-core/fastq_contam_seqtk_kraken/**
+  - subworkflows/nf-core/fastq_contam_seqtk_kraken/**
+  - tests/subworkflows/nf-core/fastq_contam_seqtk_kraken/**
 
 subworkflows/fastq_fastqc_umitools_trimgalore:
-- subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/**
-- tests/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/**
+  - subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/**
+  - tests/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/**
 
 subworkflows/gatk_create_som_pon:
-- subworkflows/nf-core/gatk_create_som_pon/**
-- tests/subworkflows/nf-core/gatk_create_som_pon/**
+  - subworkflows/nf-core/gatk_create_som_pon/**
+  - tests/subworkflows/nf-core/gatk_create_som_pon/**
 
 subworkflows/gatk_tumor_normal_somatic_variant_calling:
-- subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/**
-- tests/subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/**
+  - subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/**
+  - tests/subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/**
 
 subworkflows/gatk_tumor_only_somatic_variant_calling:
-- subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/**
-- tests/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/**
+  - subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/**
+  - tests/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/**
 
 subworkflows/homer/groseq:
-- subworkflows/nf-core/homer/groseq/**
-- tests/subworkflows/nf-core/homer/groseq/**
+  - subworkflows/nf-core/homer/groseq/**
+  - tests/subworkflows/nf-core/homer/groseq/**
 
 subworkflows/srafastq:
-- subworkflows/nf-core/srafastq/**
-- tests/subworkflows/nf-core/srafastq/**
+  - subworkflows/nf-core/srafastq/**
+  - tests/subworkflows/nf-core/srafastq/**
 
 svdb/merge:
-- modules/nf-core/svdb/merge/**
-- tests/modules/nf-core/svdb/merge/**
+  - modules/nf-core/svdb/merge/**
+  - tests/modules/nf-core/svdb/merge/**
 
 svdb/query:
-- modules/nf-core/svdb/query/**
-- tests/modules/nf-core/svdb/query/**
+  - modules/nf-core/svdb/query/**
+  - tests/modules/nf-core/svdb/query/**
 
 svtk/baftest:
-- modules/nf-core/svtk/baftest/**
-- tests/modules/nf-core/svtk/baftest/**
+  - modules/nf-core/svtk/baftest/**
+  - tests/modules/nf-core/svtk/baftest/**
 
 svtk/countsvtypes:
-- modules/nf-core/svtk/countsvtypes/**
-- tests/modules/nf-core/svtk/countsvtypes/**
+  - modules/nf-core/svtk/countsvtypes/**
+  - tests/modules/nf-core/svtk/countsvtypes/**
 
 svtk/rdtest2vcf:
-- modules/nf-core/svtk/rdtest2vcf/**
-- tests/modules/nf-core/svtk/rdtest2vcf/**
+  - modules/nf-core/svtk/rdtest2vcf/**
+  - tests/modules/nf-core/svtk/rdtest2vcf/**
 
 svtk/standardize:
-- modules/nf-core/svtk/standardize/**
-- tests/modules/nf-core/svtk/standardize/**
+  - modules/nf-core/svtk/standardize/**
+  - tests/modules/nf-core/svtk/standardize/**
 
 svtk/vcf2bed:
-- modules/nf-core/svtk/vcf2bed/**
-- tests/modules/nf-core/svtk/vcf2bed/**
+  - modules/nf-core/svtk/vcf2bed/**
+  - tests/modules/nf-core/svtk/vcf2bed/**
 
 tabix/bgzip:
-- modules/nf-core/tabix/bgzip/**
-- tests/modules/nf-core/tabix/bgzip/**
+  - modules/nf-core/tabix/bgzip/**
+  - tests/modules/nf-core/tabix/bgzip/**
 
 tabix/bgziptabix:
-- modules/nf-core/tabix/bgziptabix/**
-- tests/modules/nf-core/tabix/bgziptabix/**
+  - modules/nf-core/tabix/bgziptabix/**
+  - tests/modules/nf-core/tabix/bgziptabix/**
 
 tabix/tabix:
-- modules/nf-core/tabix/tabix/**
-- tests/modules/nf-core/tabix/tabix/**
+  - modules/nf-core/tabix/tabix/**
+  - tests/modules/nf-core/tabix/tabix/**
 
 tailfindr:
-- modules/nf-core/tailfindr/**
-- tests/modules/nf-core/tailfindr/**
+  - modules/nf-core/tailfindr/**
+  - tests/modules/nf-core/tailfindr/**
 
 tbprofiler/profile:
-- modules/nf-core/tbprofiler/profile/**
-- tests/modules/nf-core/tbprofiler/profile/**
+  - modules/nf-core/tbprofiler/profile/**
+  - tests/modules/nf-core/tbprofiler/profile/**
 
 tiddit/cov:
-- modules/nf-core/tiddit/cov/**
-- tests/modules/nf-core/tiddit/cov/**
+  - modules/nf-core/tiddit/cov/**
+  - tests/modules/nf-core/tiddit/cov/**
 
 tiddit/sv:
-- modules/nf-core/tiddit/sv/**
-- tests/modules/nf-core/tiddit/sv/**
+  - modules/nf-core/tiddit/sv/**
+  - tests/modules/nf-core/tiddit/sv/**
 
 transdecoder/longorf:
-- modules/nf-core/transdecoder/longorf/**
-- tests/modules/nf-core/transdecoder/longorf/**
+  - modules/nf-core/transdecoder/longorf/**
+  - tests/modules/nf-core/transdecoder/longorf/**
 
 transdecoder/predict:
-- modules/nf-core/transdecoder/predict/**
-- tests/modules/nf-core/transdecoder/predict/**
+  - modules/nf-core/transdecoder/predict/**
+  - tests/modules/nf-core/transdecoder/predict/**
 
 trimgalore:
-- modules/nf-core/trimgalore/**
-- tests/modules/nf-core/trimgalore/**
+  - modules/nf-core/trimgalore/**
+  - tests/modules/nf-core/trimgalore/**
 
 trimmomatic:
-- modules/nf-core/trimmomatic/**
-- tests/modules/nf-core/trimmomatic/**
+  - modules/nf-core/trimmomatic/**
+  - tests/modules/nf-core/trimmomatic/**
 
 ucsc/bedclip:
-- modules/nf-core/ucsc/bedclip/**
-- tests/modules/nf-core/ucsc/bedclip/**
+  - modules/nf-core/ucsc/bedclip/**
+  - tests/modules/nf-core/ucsc/bedclip/**
 
 ucsc/bedgraphtobigwig:
-- modules/nf-core/ucsc/bedgraphtobigwig/**
-- tests/modules/nf-core/ucsc/bedgraphtobigwig/**
+  - modules/nf-core/ucsc/bedgraphtobigwig/**
+  - tests/modules/nf-core/ucsc/bedgraphtobigwig/**
 
 ucsc/bedtobigbed:
-- modules/nf-core/ucsc/bedtobigbed/**
-- tests/modules/nf-core/ucsc/bedtobigbed/**
+  - modules/nf-core/ucsc/bedtobigbed/**
+  - tests/modules/nf-core/ucsc/bedtobigbed/**
 
 ucsc/bigwigaverageoverbed:
-- modules/nf-core/ucsc/bigwigaverageoverbed/**
-- tests/modules/nf-core/ucsc/bigwigaverageoverbed/**
+  - modules/nf-core/ucsc/bigwigaverageoverbed/**
+  - tests/modules/nf-core/ucsc/bigwigaverageoverbed/**
 
 ucsc/gtftogenepred:
-- modules/nf-core/ucsc/gtftogenepred/**
-- tests/modules/nf-core/ucsc/gtftogenepred/**
+  - modules/nf-core/ucsc/gtftogenepred/**
+  - tests/modules/nf-core/ucsc/gtftogenepred/**
 
 ucsc/liftover:
-- modules/nf-core/ucsc/liftover/**
-- tests/modules/nf-core/ucsc/liftover/**
+  - modules/nf-core/ucsc/liftover/**
+  - tests/modules/nf-core/ucsc/liftover/**
 
 ucsc/wigtobigwig:
-- modules/nf-core/ucsc/wigtobigwig/**
-- tests/modules/nf-core/ucsc/wigtobigwig/**
+  - modules/nf-core/ucsc/wigtobigwig/**
+  - tests/modules/nf-core/ucsc/wigtobigwig/**
 
 ultra/align:
-- modules/nf-core/ultra/align/**
-- tests/modules/nf-core/ultra/align/**
+  - modules/nf-core/ultra/align/**
+  - tests/modules/nf-core/ultra/align/**
 
 ultra/index:
-- modules/nf-core/ultra/index/**
-- tests/modules/nf-core/ultra/index/**
+  - modules/nf-core/ultra/index/**
+  - tests/modules/nf-core/ultra/index/**
 
 ultra/pipeline:
-- modules/nf-core/ultra/pipeline/**
-- tests/modules/nf-core/ultra/pipeline/**
+  - modules/nf-core/ultra/pipeline/**
+  - tests/modules/nf-core/ultra/pipeline/**
 
 umitools/dedup:
-- modules/nf-core/umitools/dedup/**
-- modules/nf-core/umitools/extract/**
-- tests/modules/nf-core/umitools/dedup/**
+  - modules/nf-core/umitools/dedup/**
+  - modules/nf-core/umitools/extract/**
+  - tests/modules/nf-core/umitools/dedup/**
 
 umitools/extract:
-- modules/nf-core/umitools/extract/**
-- tests/modules/nf-core/umitools/extract/**
+  - modules/nf-core/umitools/extract/**
+  - tests/modules/nf-core/umitools/extract/**
 
 unicycler:
-- modules/nf-core/unicycler/**
-- tests/modules/nf-core/unicycler/**
+  - modules/nf-core/unicycler/**
+  - tests/modules/nf-core/unicycler/**
 
 untar:
-- modules/nf-core/untar/**
-- tests/modules/nf-core/untar/**
+  - modules/nf-core/untar/**
+  - tests/modules/nf-core/untar/**
 
 unzip:
-- modules/nf-core/unzip/**
-- tests/modules/nf-core/unzip/**
+  - modules/nf-core/unzip/**
+  - tests/modules/nf-core/unzip/**
 
 vardictjava:
-- modules/nf-core/vardictjava/**
-- tests/modules/nf-core/vardictjava/**
+  - modules/nf-core/vardictjava/**
+  - tests/modules/nf-core/vardictjava/**
 
 variantbam:
-- modules/nf-core/variantbam/**
-- tests/modules/nf-core/variantbam/**
+  - modules/nf-core/variantbam/**
+  - tests/modules/nf-core/variantbam/**
 
 vcf2db:
-- modules/nf-core/vcf2db/**
-- tests/modules/nf-core/vcf2db/**
+  - modules/nf-core/vcf2db/**
+  - tests/modules/nf-core/vcf2db/**
 
 vcf2maf:
-- modules/nf-core/vcf2maf/**
-- tests/modules/nf-core/vcf2maf/**
+  - modules/nf-core/vcf2maf/**
+  - tests/modules/nf-core/vcf2maf/**
 
 vcfanno:
-- modules/nf-core/vcfanno/**
-- tests/modules/nf-core/vcfanno/**
+  - modules/nf-core/vcfanno/**
+  - tests/modules/nf-core/vcfanno/**
 
 vcflib/vcfbreakmulti:
-- modules/nf-core/vcflib/vcfbreakmulti/**
-- tests/modules/nf-core/vcflib/vcfbreakmulti/**
+  - modules/nf-core/vcflib/vcfbreakmulti/**
+  - tests/modules/nf-core/vcflib/vcfbreakmulti/**
 
 vcflib/vcfuniq:
-- modules/nf-core/vcflib/vcfuniq/**
-- tests/modules/nf-core/vcflib/vcfuniq/**
+  - modules/nf-core/vcflib/vcfuniq/**
+  - tests/modules/nf-core/vcflib/vcfuniq/**
 
 vcftools:
-- modules/nf-core/vcftools/**
-- tests/modules/nf-core/vcftools/**
+  - modules/nf-core/vcftools/**
+  - tests/modules/nf-core/vcftools/**
 
 verifybamid/verifybamid2:
-- modules/nf-core/verifybamid/verifybamid2/**
-- tests/modules/nf-core/verifybamid/verifybamid2/**
+  - modules/nf-core/verifybamid/verifybamid2/**
+  - tests/modules/nf-core/verifybamid/verifybamid2/**
 
 vg/deconstruct:
-- modules/nf-core/vg/deconstruct/**
-- tests/modules/nf-core/vg/deconstruct/**
+  - modules/nf-core/vg/deconstruct/**
+  - tests/modules/nf-core/vg/deconstruct/**
 
 vsearch/cluster:
-- modules/nf-core/vsearch/cluster/**
-- tests/modules/nf-core/vsearch/cluster/**
+  - modules/nf-core/vsearch/cluster/**
+  - tests/modules/nf-core/vsearch/cluster/**
 
 vsearch/sintax:
-- modules/nf-core/vsearch/sintax/**
-- tests/modules/nf-core/vsearch/sintax/**
+  - modules/nf-core/vsearch/sintax/**
+  - tests/modules/nf-core/vsearch/sintax/**
 
 vsearch/usearchglobal:
-- modules/nf-core/vsearch/usearchglobal/**
-- tests/modules/nf-core/vsearch/usearchglobal/**
+  - modules/nf-core/vsearch/usearchglobal/**
+  - tests/modules/nf-core/vsearch/usearchglobal/**
 
 wgsim:
-- modules/nf-core/wgsim/**
-- tests/modules/nf-core/wgsim/**
+  - modules/nf-core/wgsim/**
+  - tests/modules/nf-core/wgsim/**
 
 whamg:
-- modules/nf-core/whamg/**
-- tests/modules/nf-core/whamg/**
+  - modules/nf-core/whamg/**
+  - tests/modules/nf-core/whamg/**
 
 yara/index:
-- modules/nf-core/yara/index/**
-- tests/modules/nf-core/yara/index/**
+  - modules/nf-core/yara/index/**
+  - tests/modules/nf-core/yara/index/**
 
 yara/mapper:
-- modules/nf-core/yara/mapper/**
-- tests/modules/nf-core/yara/mapper/**
+  - modules/nf-core/yara/mapper/**
+  - tests/modules/nf-core/yara/mapper/**

From b111ed2dfb6c6f6895d69f36eaa1311d590755b4 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Tue, 17 Jan 2023 15:08:16 -0500
Subject: [PATCH 054/114] added more accurate input pattern

---
 modules/nf-core/ashlar/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/ashlar/meta.yml b/modules/nf-core/ashlar/meta.yml
index a6dcd65a991..2b46ba18f3e 100644
--- a/modules/nf-core/ashlar/meta.yml
+++ b/modules/nf-core/ashlar/meta.yml
@@ -21,7 +21,7 @@ input:
   - file_in:
       type: path
       description: multidimentional image data in formats from most commercial microscopes
-      pattern: "*.ome.tiff"
+      pattern: "*.{ome.tif, ome.tiff, tif, tiff}"
 
 output:
   #

From b3fbd521cf9d195613909df9325294c6e996cfe0 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Tue, 14 Mar 2023 14:56:50 -0400
Subject: [PATCH 055/114] works with new test images

---
 modules/nf-core/ashlar/main.nf       |  9 +-------
 tests/modules/nf-core/ashlar/main.nf | 31 +++++++++++++++++++++-------
 2 files changed, 25 insertions(+), 15 deletions(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 69a222ab005..b8f996f0ac8 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -3,14 +3,7 @@ process ASHLAR {
     label 'process_single'
 
     conda (params.enable_conda ? "bioconda::ashlar=1.17.0" : null)
-    /* TODO nf-core: we'll provide a dockerfile as described in 5) under Software Requirements
-                     at https://nf-co.re/developers/modules#software-requirements
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ashlar':
-        'quay.io/biocontainers/ashlar' }"
-
-    container 'ghcr.io/????/ashlar:1.17.0'
-    */
+    container 'docker.io/labsyspharm/ashlar:1.17.0'
 
     input:
     tuple val(meta), val(file_in)
diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index f5758d32619..198a9d4f64b 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -6,11 +6,16 @@ include { ASHLAR } from '../../../../../modules/modules/nf-core/ashlar/main.nf'
 // we zero out the UUID of output tiff images with ZERO_UUID so we get a consistent md5sum
 include { ZERO_UUID } from './zero_uuid.nf'
 
-def TEST_IMG = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-0{6,7}.ome.tiff"
-def TEST_IMG_1 = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-06.ome.tiff"
-def TEST_IMG_2 = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-07.ome.tiff"
-def TEST_DFP_1 = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/illumination/exemplar-001-cycle-06-dfp.tif"
-def TEST_FFP_1 = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/illumination/exemplar-001-cycle-06-ffp.tif"
+def TEST_ORIG_IMG = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-0{6,7}.ome.tiff"
+def TEST_ORIG_IMG_1 = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-06.ome.tiff"
+def TEST_ORIG_IMG_2 = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-07.ome.tiff"
+def TEST_ORIG_DFP_1 = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/illumination/exemplar-001-cycle-06-dfp.tif"
+def TEST_ORIG_FFP_1 = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/illumination/exemplar-001-cycle-06-ffp.tif"
+
+def TEST_IMG_ALL = "/home/pollen/HITS/nextflow/mcmicro/cycif-tonsil/cycif-tonsil-cycle{1,2,3}.ome.tif"
+def TEST_IMG_1 = "/home/pollen/HITS/nextflow/mcmicro/cycif-tonsil/cycif-tonsil-cycle1.ome.tif"
+def TEST_IMG_2 = "/home/pollen/HITS/nextflow/mcmicro/cycif-tonsil/cycif-tonsil-cycle2.ome.tif"
+def TEST_IMG_3 = "/home/pollen/HITS/nextflow/mcmicro/cycif-tonsil/cycif-tonsil-cycle3.ome.tif"
 
 workflow test_ashlar_one_file {
 
@@ -36,6 +41,18 @@ workflow test_ashlar_two_files {
 
 }
 
+workflow test_ashlar_all_files {
+
+    input_list =  [ [ [ id:'test_2', args: '--flip-x' ],
+               "${TEST_IMG_ALL}" ] ]
+    input_channel = Channel.fromList(input_list)
+
+    ASHLAR ( input_channel )
+
+    ZERO_UUID ( ASHLAR.out[1] )
+
+}
+
 workflow test_ashlar_align_channel {
 
     input_list =  [ [ [ id:'test_1', args: '--align-channel 1' ],
@@ -50,8 +67,8 @@ workflow test_ashlar_align_channel {
 
 workflow test_ashlar_dfp_ffp {
 
-    input_list =  [ [ [ id:'test_1', args: "--dfp ${TEST_DFP_1} --ffp ${TEST_FFP_1}" ],
-               "${TEST_IMG_1}" ] ]
+    input_list =  [ [ [ id:'test_1', args: "--dfp ${TEST_ORIG_DFP_1} --ffp ${TEST_ORIG_FFP_1}" ],
+               "${TEST_ORIG_IMG_1}" ] ]
     input_channel = Channel.fromList(input_list)
 
     ASHLAR ( input_channel )

From a5165c6dc4ceb57a36957e00b37678dfb437a2e0 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Tue, 14 Mar 2023 18:23:42 -0400
Subject: [PATCH 056/114] added test.yml

---
 tests/modules/nf-core/ashlar/test.yml | 44 +++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)
 create mode 100644 tests/modules/nf-core/ashlar/test.yml

diff --git a/tests/modules/nf-core/ashlar/test.yml b/tests/modules/nf-core/ashlar/test.yml
new file mode 100644
index 00000000000..a29ab024608
--- /dev/null
+++ b/tests/modules/nf-core/ashlar/test.yml
@@ -0,0 +1,44 @@
+- name: ashlar test_ashlar_one_file
+  command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_one_file -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
+  tags:
+    - ashlar
+  files:
+    - path: output/ashlar/ashlar_output.ome.tif
+      md5sum: b47c1f36149067a100782fe43da8aebf
+    - path: output/ashlar/versions.yml
+
+- name: ashlar test_ashlar_two_files
+  command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_two_files -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
+  tags:
+    - ashlar
+  files:
+    - path: output/ashlar/ashlar_output.ome.tif
+      md5sum: ccdf8734a3df0c62699a84d96ad93bfb
+    - path: output/ashlar/versions.yml
+
+- name: ashlar test_ashlar_all_files
+  command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_all_files -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
+  tags:
+    - ashlar
+  files:
+    - path: output/ashlar/ashlar_output.ome.tif
+      md5sum: 544cb8ab6b5482920a6caa6b47b57305
+    - path: output/ashlar/versions.yml
+
+- name: ashlar test_ashlar_align_channel
+  command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_align_channel -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
+  tags:
+    - ashlar
+  files:
+    - path: output/ashlar/ashlar_output.ome.tif
+      md5sum: 091d3230e3d01282ad6659aff195deba
+    - path: output/ashlar/versions.yml
+
+- name: ashlar test_ashlar_dfp_ffp
+  command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_dfp_ffp -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
+  tags:
+    - ashlar
+  files:
+    - path: output/ashlar/ashlar_output.ome.tif
+      md5sum: 41fd86599d6fc10aa4393303c497505e
+    - path: output/ashlar/versions.yml

From 5487b2c483fa21c410531d258de358fac9d86fec Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Wed, 15 Mar 2023 15:43:14 -0400
Subject: [PATCH 057/114] removed unsupported output test and updated input and
 output patterns in meta; tests pass

---
 modules/nf-core/ashlar/meta.yml       | 5 ++---
 tests/modules/nf-core/ashlar/main.nf  | 1 +
 tests/modules/nf-core/ashlar/test.yml | 6 +++---
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/modules/nf-core/ashlar/meta.yml b/modules/nf-core/ashlar/meta.yml
index 2b46ba18f3e..3fe6f3d3deb 100644
--- a/modules/nf-core/ashlar/meta.yml
+++ b/modules/nf-core/ashlar/meta.yml
@@ -21,8 +21,7 @@ input:
   - file_in:
       type: path
       description: multidimentional image data in formats from most commercial microscopes
-      pattern: "*.{ome.tif, ome.tiff, tif, tiff}"
-
+      pattern: "*.{ome.tiff,ome.tif,rcpnl,btf,nd2,tiff,tif,czi}"
 output:
   #
   - meta:
@@ -33,7 +32,7 @@ output:
   - file_out:
       type: file
       description: pyramidal OME-TIFF
-      pattern: "*.tif"
+      pattern: "*.ome.tif"
   - versions:
       type: file
       description: File containing software versions
diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index 198a9d4f64b..8bd6649029b 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -76,3 +76,4 @@ workflow test_ashlar_dfp_ffp {
     ZERO_UUID ( ASHLAR.out[1] )
 
 }
+
diff --git a/tests/modules/nf-core/ashlar/test.yml b/tests/modules/nf-core/ashlar/test.yml
index a29ab024608..06c3f12881d 100644
--- a/tests/modules/nf-core/ashlar/test.yml
+++ b/tests/modules/nf-core/ashlar/test.yml
@@ -4,7 +4,7 @@
     - ashlar
   files:
     - path: output/ashlar/ashlar_output.ome.tif
-      md5sum: b47c1f36149067a100782fe43da8aebf
+      md5sum: 4249e2c458f8fc9ee4ea90a6869acec0
     - path: output/ashlar/versions.yml
 
 - name: ashlar test_ashlar_two_files
@@ -13,7 +13,7 @@
     - ashlar
   files:
     - path: output/ashlar/ashlar_output.ome.tif
-      md5sum: ccdf8734a3df0c62699a84d96ad93bfb
+      md5sum: fcd46d75234a76c1949787b698db6af6
     - path: output/ashlar/versions.yml
 
 - name: ashlar test_ashlar_all_files
@@ -31,7 +31,7 @@
     - ashlar
   files:
     - path: output/ashlar/ashlar_output.ome.tif
-      md5sum: 091d3230e3d01282ad6659aff195deba
+      md5sum: f52a19069cc13b916868f50605651832
     - path: output/ashlar/versions.yml
 
 - name: ashlar test_ashlar_dfp_ffp

From 95160c500febbd9799b98be32ba07723ca01fb93 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Fri, 17 Mar 2023 13:00:20 -0400
Subject: [PATCH 058/114] refactored zero_uuid.nf to use input parameter
 offset; passed test

---
 tests/modules/nf-core/ashlar/main.nf      | 52 +----------------------
 tests/modules/nf-core/ashlar/test.yml     | 36 ----------------
 tests/modules/nf-core/ashlar/zero_uuid.nf | 31 +++++---------
 3 files changed, 13 insertions(+), 106 deletions(-)

diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index 8bd6649029b..904ce7c82b0 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -17,63 +17,15 @@ def TEST_IMG_1 = "/home/pollen/HITS/nextflow/mcmicro/cycif-tonsil/cycif-tonsil-c
 def TEST_IMG_2 = "/home/pollen/HITS/nextflow/mcmicro/cycif-tonsil/cycif-tonsil-cycle2.ome.tif"
 def TEST_IMG_3 = "/home/pollen/HITS/nextflow/mcmicro/cycif-tonsil/cycif-tonsil-cycle3.ome.tif"
 
-workflow test_ashlar_one_file {
-
-    input_list =  [ [ [ id:'test_1', args: '--flip-y' ],
-               "${TEST_IMG_1}" ] ]
-    input_channel = Channel.fromList(input_list)
-
-    ASHLAR ( input_channel )
-
-    ZERO_UUID ( ASHLAR.out[1] )
-
-}
-
-workflow test_ashlar_two_files {
-
-    input_list =  [ [ [ id:'test_2', args: '--flip-x' ],
-               "${TEST_IMG_1} ${TEST_IMG_2}" ] ]
-    input_channel = Channel.fromList(input_list)
-
-    ASHLAR ( input_channel )
-
-    ZERO_UUID ( ASHLAR.out[1] )
-
-}
-
 workflow test_ashlar_all_files {
 
-    input_list =  [ [ [ id:'test_2', args: '--flip-x' ],
+    input_list =  [ [ [ id:'test_all', args: '' ],
                "${TEST_IMG_ALL}" ] ]
     input_channel = Channel.fromList(input_list)
 
     ASHLAR ( input_channel )
 
-    ZERO_UUID ( ASHLAR.out[1] )
-
-}
-
-workflow test_ashlar_align_channel {
-
-    input_list =  [ [ [ id:'test_1', args: '--align-channel 1' ],
-               "${TEST_IMG_1}" ] ]
-    input_channel = Channel.fromList(input_list)
-
-    ASHLAR ( input_channel )
-
-    ZERO_UUID ( ASHLAR.out[1] )
-
-}
-
-workflow test_ashlar_dfp_ffp {
-
-    input_list =  [ [ [ id:'test_1', args: "--dfp ${TEST_ORIG_DFP_1} --ffp ${TEST_ORIG_FFP_1}" ],
-               "${TEST_ORIG_IMG_1}" ] ]
-    input_channel = Channel.fromList(input_list)
-
-    ASHLAR ( input_channel )
-
-    ZERO_UUID ( ASHLAR.out[1] )
+    ZERO_UUID ( ASHLAR.out[0], "25169643" )
 
 }
 
diff --git a/tests/modules/nf-core/ashlar/test.yml b/tests/modules/nf-core/ashlar/test.yml
index 06c3f12881d..e3f63b7abf7 100644
--- a/tests/modules/nf-core/ashlar/test.yml
+++ b/tests/modules/nf-core/ashlar/test.yml
@@ -1,21 +1,3 @@
-- name: ashlar test_ashlar_one_file
-  command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_one_file -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
-  tags:
-    - ashlar
-  files:
-    - path: output/ashlar/ashlar_output.ome.tif
-      md5sum: 4249e2c458f8fc9ee4ea90a6869acec0
-    - path: output/ashlar/versions.yml
-
-- name: ashlar test_ashlar_two_files
-  command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_two_files -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
-  tags:
-    - ashlar
-  files:
-    - path: output/ashlar/ashlar_output.ome.tif
-      md5sum: fcd46d75234a76c1949787b698db6af6
-    - path: output/ashlar/versions.yml
-
 - name: ashlar test_ashlar_all_files
   command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_all_files -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
   tags:
@@ -24,21 +6,3 @@
     - path: output/ashlar/ashlar_output.ome.tif
       md5sum: 544cb8ab6b5482920a6caa6b47b57305
     - path: output/ashlar/versions.yml
-
-- name: ashlar test_ashlar_align_channel
-  command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_align_channel -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
-  tags:
-    - ashlar
-  files:
-    - path: output/ashlar/ashlar_output.ome.tif
-      md5sum: f52a19069cc13b916868f50605651832
-    - path: output/ashlar/versions.yml
-
-- name: ashlar test_ashlar_dfp_ffp
-  command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_dfp_ffp -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
-  tags:
-    - ashlar
-  files:
-    - path: output/ashlar/ashlar_output.ome.tif
-      md5sum: 41fd86599d6fc10aa4393303c497505e
-    - path: output/ashlar/versions.yml
diff --git a/tests/modules/nf-core/ashlar/zero_uuid.nf b/tests/modules/nf-core/ashlar/zero_uuid.nf
index d7c2fb2fc5c..e480585de93 100644
--- a/tests/modules/nf-core/ashlar/zero_uuid.nf
+++ b/tests/modules/nf-core/ashlar/zero_uuid.nf
@@ -3,29 +3,20 @@ nextflow.enable.dsl=2
 process ZERO_UUID {
 
     input:
-    each path(file_in)
+    val(file_in)
+    val(offset)
+
+    when:
+    file_in != "versions.yml"
 
     script:
     """
-    TARG_PATHS_ARRAY=(\$(find ../.. -name "ashlar_output.ome.tif" -printf "%k %p\n" | sort -n | awk -F ' ' '{print \$2}'))
-    TARG_ARRAY_LEN=\${#TARG_PATHS_ARRAY[@]}
-    if [[ \$(( \$TARG_ARRAY_LEN % 2 )) != 0 ]]; then
-        exit 0
-    fi
-
-    for (( idx=0; idx<\${TARG_ARRAY_LEN}; idx+=2 )); do
-        TARG_OFFSET=\$(cmp "\${TARG_PATHS_ARRAY[\$idx]}" "\${TARG_PATHS_ARRAY[\$idx+1]}" | awk -F ' ' '{print substr(\$5,1,length(\$5)-1)}')
-        if [ \$TARG_OFFSET ]; then
-            TARG_OFFSET="\$((TARG_OFFSET - 1))"
-            echo -n "00000000-0000-0000-0000-000000000000" | dd of=\${TARG_PATHS_ARRAY[\$idx]} bs=1 seek=\${TARG_OFFSET} conv=notrunc
-            echo -n "00000000-0000-0000-0000-000000000000" | dd of=\${TARG_PATHS_ARRAY[\$idx+1]} bs=1 seek=\${TARG_OFFSET} conv=notrunc
-        fi
-        TARG_OFFSET=\$(cmp "\${TARG_PATHS_ARRAY[\$idx]}" "\${TARG_PATHS_ARRAY[\$idx+1]}" | awk -F ' ' '{print substr(\$5,1,length(\$5)-1)}')
-        if [ \$TARG_OFFSET ]; then
-            echo "Error: files still different after UUID update!"
-        fi
-
-    done
+
+    IFS=',' read -ra FILE_IN_ARRAY <<< "$file_in"
+    FILE_PATH_REMOVED_PREFIX="/\${FILE_IN_ARRAY[2]#*/}"
+    FILE_PATH=\${FILE_PATH_REMOVED_PREFIX::-1}
+
+    echo -n "00000000-0000-0000-0000-000000000000" | dd of=\${FILE_PATH} bs=1 seek=$offset conv=notrunc
 
     """
 

From 2d9411c2b8e96ad6e3a331adc1d2668ddd525b13 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Fri, 17 Mar 2023 15:55:31 -0400
Subject: [PATCH 059/114] added tile size test as discussed in PR

---
 tests/modules/nf-core/ashlar/main.nf  | 11 +++++++++++
 tests/modules/nf-core/ashlar/test.yml |  9 +++++++++
 2 files changed, 20 insertions(+)

diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index 904ce7c82b0..6181f7617c4 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -29,3 +29,14 @@ workflow test_ashlar_all_files {
 
 }
 
+workflow test_ashlar_all_files_tile_size {
+
+    input_list =  [ [ [ id:'test_all_tile_size', args: '--tile-size 512' ],
+               "${TEST_IMG_ALL}" ] ]
+    input_channel = Channel.fromList(input_list)
+
+    ASHLAR ( input_channel )
+
+    ZERO_UUID ( ASHLAR.out[0], "6295276" )
+
+}
diff --git a/tests/modules/nf-core/ashlar/test.yml b/tests/modules/nf-core/ashlar/test.yml
index e3f63b7abf7..443a5f3743c 100644
--- a/tests/modules/nf-core/ashlar/test.yml
+++ b/tests/modules/nf-core/ashlar/test.yml
@@ -6,3 +6,12 @@
     - path: output/ashlar/ashlar_output.ome.tif
       md5sum: 544cb8ab6b5482920a6caa6b47b57305
     - path: output/ashlar/versions.yml
+
+- name: ashlar test_ashlar_all_files_tile_size
+  command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_all_files_tile_size -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
+  tags:
+    - ashlar
+  files:
+    - path: output/ashlar/ashlar_output.ome.tif
+      md5sum: 1139e042060c92691b93d6bbc8ae4d72
+    - path: output/ashlar/versions.yml

From 79a1ef4b2263eca646df8a688cfa28dc73d83f21 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Fri, 17 Mar 2023 17:15:31 -0400
Subject: [PATCH 060/114] bug fix: off by one error for second test offset

---
 tests/modules/nf-core/ashlar/main.nf  | 2 +-
 tests/modules/nf-core/ashlar/test.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index 6181f7617c4..3fcd209d107 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -37,6 +37,6 @@ workflow test_ashlar_all_files_tile_size {
 
     ASHLAR ( input_channel )
 
-    ZERO_UUID ( ASHLAR.out[0], "6295276" )
+    ZERO_UUID ( ASHLAR.out[0], "6295275" )
 
 }
diff --git a/tests/modules/nf-core/ashlar/test.yml b/tests/modules/nf-core/ashlar/test.yml
index 443a5f3743c..49c0aa586f4 100644
--- a/tests/modules/nf-core/ashlar/test.yml
+++ b/tests/modules/nf-core/ashlar/test.yml
@@ -13,5 +13,5 @@
     - ashlar
   files:
     - path: output/ashlar/ashlar_output.ome.tif
-      md5sum: 1139e042060c92691b93d6bbc8ae4d72
+      md5sum: 51dc4435dfd3e7ef23e20e66ca70c4be
     - path: output/ashlar/versions.yml

From 2c133d6945f71b8c08ee38f5e884e25d7de76348 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Mon, 20 Mar 2023 17:36:52 -0400
Subject: [PATCH 061/114] clean-up

---
 modules/nf-core/ashlar/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index b8f996f0ac8..10c9f84a5e8 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -9,7 +9,7 @@ process ASHLAR {
     tuple val(meta), val(file_in)
 
     output:
-    tuple val(meta), path("*.tif")  ,   emit: ashlar_tif
+    tuple val(meta), path("*.tif")      ,   emit: ashlar_tif
     path "versions.yml"                 ,   emit: versions
 
     when:

From 08281272dc7253e6dfc62f5a4ce40ca65ba6d2a8 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Tue, 21 Mar 2023 14:12:32 -0400
Subject: [PATCH 062/114] simplified zero_uuid.nf

---
 tests/modules/nf-core/ashlar/zero_uuid.nf | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/tests/modules/nf-core/ashlar/zero_uuid.nf b/tests/modules/nf-core/ashlar/zero_uuid.nf
index e480585de93..de6ddc5a452 100644
--- a/tests/modules/nf-core/ashlar/zero_uuid.nf
+++ b/tests/modules/nf-core/ashlar/zero_uuid.nf
@@ -10,13 +10,11 @@ process ZERO_UUID {
     file_in != "versions.yml"
 
     script:
-    """
+    def file_path = file_in[1]
 
-    IFS=',' read -ra FILE_IN_ARRAY <<< "$file_in"
-    FILE_PATH_REMOVED_PREFIX="/\${FILE_IN_ARRAY[2]#*/}"
-    FILE_PATH=\${FILE_PATH_REMOVED_PREFIX::-1}
+    """
 
-    echo -n "00000000-0000-0000-0000-000000000000" | dd of=\${FILE_PATH} bs=1 seek=$offset conv=notrunc
+    echo -n "00000000-0000-0000-0000-000000000000" | dd of=$file_path bs=1 seek=$offset conv=notrunc
 
     """
 

From c908aeac38b3a42caa79096fd4d662364d0b4eaf Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Fri, 31 Mar 2023 15:20:23 -0400
Subject: [PATCH 063/114] changed to built-in test files

+ use built-in test files
+ changed input parameter to path from val
+ removed input parameter from nextflow.confg
---
 modules/nf-core/ashlar/main.nf               |  5 ++-
 tests/modules/nf-core/ashlar/main.nf         | 33 +++++++++++---------
 tests/modules/nf-core/ashlar/nextflow.config |  2 +-
 tests/modules/nf-core/ashlar/test.yml        | 13 ++++++--
 4 files changed, 33 insertions(+), 20 deletions(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 10c9f84a5e8..14b0526ac3f 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -2,11 +2,10 @@ process ASHLAR {
     tag '$meta.id'
     label 'process_single'
 
-    conda (params.enable_conda ? "bioconda::ashlar=1.17.0" : null)
-    container 'docker.io/labsyspharm/ashlar:1.17.0'
+    conda "bioconda::ashlar=1.17.0"
 
     input:
-    tuple val(meta), val(file_in)
+    tuple val(meta), path(file_in)
 
     output:
     tuple val(meta), path("*.tif")      ,   emit: ashlar_tif
diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index 3fcd209d107..09630ac97c7 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -2,25 +2,28 @@
 
 nextflow.enable.dsl = 2
 
-include { ASHLAR } from '../../../../../modules/modules/nf-core/ashlar/main.nf'
+include { ASHLAR } from '../../../../modules/nf-core/ashlar/main.nf'
 // we zero out the UUID of output tiff images with ZERO_UUID so we get a consistent md5sum
 include { ZERO_UUID } from './zero_uuid.nf'
 
-def TEST_ORIG_IMG = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-0{6,7}.ome.tiff"
-def TEST_ORIG_IMG_1 = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-06.ome.tiff"
-def TEST_ORIG_IMG_2 = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/raw/exemplar-001-cycle-07.ome.tiff"
-def TEST_ORIG_DFP_1 = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/illumination/exemplar-001-cycle-06-dfp.tif"
-def TEST_ORIG_FFP_1 = "/home/pollen/HITS/nextflow/mcmicro/exemplar-001/illumination/exemplar-001-cycle-06-ffp.tif"
+workflow test_ashlar_1_file {
 
-def TEST_IMG_ALL = "/home/pollen/HITS/nextflow/mcmicro/cycif-tonsil/cycif-tonsil-cycle{1,2,3}.ome.tif"
-def TEST_IMG_1 = "/home/pollen/HITS/nextflow/mcmicro/cycif-tonsil/cycif-tonsil-cycle1.ome.tif"
-def TEST_IMG_2 = "/home/pollen/HITS/nextflow/mcmicro/cycif-tonsil/cycif-tonsil-cycle2.ome.tif"
-def TEST_IMG_3 = "/home/pollen/HITS/nextflow/mcmicro/cycif-tonsil/cycif-tonsil-cycle3.ome.tif"
+    input_list =  [ [ [ id:'test_all', args: '' ],
+               [file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle1'], checkIfExists: true)] ] ]
+    input_channel = Channel.fromList(input_list)
+
+    ASHLAR ( input_channel )
+
+    ZERO_UUID ( ASHLAR.out[0], "8390123" )
+
+}
 
 workflow test_ashlar_all_files {
 
     input_list =  [ [ [ id:'test_all', args: '' ],
-               "${TEST_IMG_ALL}" ] ]
+               [file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle1'], checkIfExists: true),
+                file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle2'], checkIfExists: true),
+                file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle3'], checkIfExists: true)] ] ]
     input_channel = Channel.fromList(input_list)
 
     ASHLAR ( input_channel )
@@ -31,12 +34,14 @@ workflow test_ashlar_all_files {
 
 workflow test_ashlar_all_files_tile_size {
 
-    input_list =  [ [ [ id:'test_all_tile_size', args: '--tile-size 512' ],
-               "${TEST_IMG_ALL}" ] ]
+    input_list =  [ [ [ id:'test_all', args: '--tile-size 512' ],
+               [file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle1'], checkIfExists: true),
+                file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle2'], checkIfExists: true),
+                file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle3'], checkIfExists: true)] ] ]
     input_channel = Channel.fromList(input_list)
 
     ASHLAR ( input_channel )
 
-    ZERO_UUID ( ASHLAR.out[0], "6295275" )
+    ZERO_UUID ( ASHLAR.out[0], "12586923" )
 
 }
diff --git a/tests/modules/nf-core/ashlar/nextflow.config b/tests/modules/nf-core/ashlar/nextflow.config
index 581f49321e5..2f39c310f4c 100644
--- a/tests/modules/nf-core/ashlar/nextflow.config
+++ b/tests/modules/nf-core/ashlar/nextflow.config
@@ -2,6 +2,6 @@ process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
-    ext.args = "--flip-x"
+    ext.args = ""
 
 }
diff --git a/tests/modules/nf-core/ashlar/test.yml b/tests/modules/nf-core/ashlar/test.yml
index 49c0aa586f4..6803a937ef0 100644
--- a/tests/modules/nf-core/ashlar/test.yml
+++ b/tests/modules/nf-core/ashlar/test.yml
@@ -1,10 +1,19 @@
+- name: ashlar test_ashlar_1_file
+  command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_1_file -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
+  tags:
+    - ashlar
+  files:
+    - path: output/ashlar/ashlar_output.ome.tif
+      md5sum: 796fa3687d4ff1389567c22eafb1e4cf
+    - path: output/ashlar/versions.yml
+
 - name: ashlar test_ashlar_all_files
   command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_all_files -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
   tags:
     - ashlar
   files:
     - path: output/ashlar/ashlar_output.ome.tif
-      md5sum: 544cb8ab6b5482920a6caa6b47b57305
+      md5sum: 576bc81fa8d678547e87d25c403ed3a4
     - path: output/ashlar/versions.yml
 
 - name: ashlar test_ashlar_all_files_tile_size
@@ -13,5 +22,5 @@
     - ashlar
   files:
     - path: output/ashlar/ashlar_output.ome.tif
-      md5sum: 51dc4435dfd3e7ef23e20e66ca70c4be
+      md5sum: fb34bb112d0c95698afa76095e12085f
     - path: output/ashlar/versions.yml

From 5c3ce93e33407da8a7890ead5de2840c605e6bec Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Fri, 31 Mar 2023 15:23:44 -0400
Subject: [PATCH 064/114] removed conda command so runs locally

Sorry, didn't mean to push the last commit.
This one has the changes and runs fine locally.  The previous commit fails because of 'conda "bioconda::ashlar=1.17.0"' in main.nf.  Seems that it fails to build the local conda environment.
---
 modules/nf-core/ashlar/main.nf | 2 --
 1 file changed, 2 deletions(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 14b0526ac3f..aeba57628ff 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -2,8 +2,6 @@ process ASHLAR {
     tag '$meta.id'
     label 'process_single'
 
-    conda "bioconda::ashlar=1.17.0"
-
     input:
     tuple val(meta), path(file_in)
 

From f1a99f2c5b956630188ae9c966584d1c753401e5 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Fri, 31 Mar 2023 15:42:53 -0400
Subject: [PATCH 065/114] added commented code that causes break

---
 modules/nf-core/ashlar/main.nf | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index aeba57628ff..0f8447dc2e8 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -2,6 +2,13 @@ process ASHLAR {
     tag '$meta.id'
     label 'process_single'
 
+    /*
+    conda "bioconda::ashlar=1.17.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ashlar:1.17.0' :
+        'quay.io/biocontainers/ashlar:1.17.0' }"
+    */
+    
     input:
     tuple val(meta), path(file_in)
 

From b26f50a132b0701d195484d18df2c3920d94e374 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Fri, 31 Mar 2023 17:07:37 -0400
Subject: [PATCH 066/114] works in linux with conda so uncommented that section

---
 modules/nf-core/ashlar/main.nf        |  5 +++--
 tests/modules/nf-core/ashlar/test.yml | 21 +++++++++------------
 2 files changed, 12 insertions(+), 14 deletions(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 0f8447dc2e8..4ef0306813c 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -2,13 +2,14 @@ process ASHLAR {
     tag '$meta.id'
     label 'process_single'
 
-    /*
     conda "bioconda::ashlar=1.17.0"
+
+    /*
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ashlar:1.17.0' :
         'quay.io/biocontainers/ashlar:1.17.0' }"
     */
-    
+
     input:
     tuple val(meta), path(file_in)
 
diff --git a/tests/modules/nf-core/ashlar/test.yml b/tests/modules/nf-core/ashlar/test.yml
index 6803a937ef0..dad40f1c8c7 100644
--- a/tests/modules/nf-core/ashlar/test.yml
+++ b/tests/modules/nf-core/ashlar/test.yml
@@ -1,26 +1,23 @@
 - name: ashlar test_ashlar_1_file
   command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_1_file -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
   tags:
-    - ashlar
+  - ashlar
   files:
-    - path: output/ashlar/ashlar_output.ome.tif
-      md5sum: 796fa3687d4ff1389567c22eafb1e4cf
-    - path: output/ashlar/versions.yml
+  - path: output/ashlar/ashlar_output.ome.tif
+    md5sum: 796fa3687d4ff1389567c22eafb1e4cf
 
 - name: ashlar test_ashlar_all_files
   command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_all_files -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
   tags:
-    - ashlar
+  - ashlar
   files:
-    - path: output/ashlar/ashlar_output.ome.tif
-      md5sum: 576bc81fa8d678547e87d25c403ed3a4
-    - path: output/ashlar/versions.yml
+  - path: output/ashlar/ashlar_output.ome.tif
+    md5sum: 576bc81fa8d678547e87d25c403ed3a4
 
 - name: ashlar test_ashlar_all_files_tile_size
   command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_all_files_tile_size -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
   tags:
-    - ashlar
+  - ashlar
   files:
-    - path: output/ashlar/ashlar_output.ome.tif
-      md5sum: fb34bb112d0c95698afa76095e12085f
-    - path: output/ashlar/versions.yml
+  - path: output/ashlar/ashlar_output.ome.tif
+    md5sum: fb34bb112d0c95698afa76095e12085f

From f5675467a1c31bbcb96f6d246fa624ba91049682 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Mon, 3 Apr 2023 11:20:09 -0400
Subject: [PATCH 067/114] added containers and tested all 3 ways of running;
 all working

---
 modules/nf-core/ashlar/main.nf | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 4ef0306813c..db2e1436d59 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -3,12 +3,10 @@ process ASHLAR {
     label 'process_single'
 
     conda "bioconda::ashlar=1.17.0"
-
-    /*
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ashlar:1.17.0' :
-        'quay.io/biocontainers/ashlar:1.17.0' }"
-    */
+        'https://depot.galaxyproject.org/singularity/ashlar:1.17.0--pyh5e36f6f_0' :
+        'quay.io/biocontainers/ashlar:1.17.0--pyh5e36f6f_0' }"
+
 
     input:
     tuple val(meta), path(file_in)

From 77d4e0fd18c41698bccefddf36bd29ba75564a01 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Tue, 16 May 2023 11:56:47 -0400
Subject: [PATCH 068/114] ran prettier

---
 tests/modules/nf-core/ashlar/test.yml | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/tests/modules/nf-core/ashlar/test.yml b/tests/modules/nf-core/ashlar/test.yml
index dad40f1c8c7..35f837ded1e 100644
--- a/tests/modules/nf-core/ashlar/test.yml
+++ b/tests/modules/nf-core/ashlar/test.yml
@@ -1,23 +1,23 @@
 - name: ashlar test_ashlar_1_file
   command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_1_file -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
   tags:
-  - ashlar
+    - ashlar
   files:
-  - path: output/ashlar/ashlar_output.ome.tif
-    md5sum: 796fa3687d4ff1389567c22eafb1e4cf
+    - path: output/ashlar/ashlar_output.ome.tif
+      md5sum: 796fa3687d4ff1389567c22eafb1e4cf
 
 - name: ashlar test_ashlar_all_files
   command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_all_files -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
   tags:
-  - ashlar
+    - ashlar
   files:
-  - path: output/ashlar/ashlar_output.ome.tif
-    md5sum: 576bc81fa8d678547e87d25c403ed3a4
+    - path: output/ashlar/ashlar_output.ome.tif
+      md5sum: 576bc81fa8d678547e87d25c403ed3a4
 
 - name: ashlar test_ashlar_all_files_tile_size
   command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_all_files_tile_size -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
   tags:
-  - ashlar
+    - ashlar
   files:
-  - path: output/ashlar/ashlar_output.ome.tif
-    md5sum: fb34bb112d0c95698afa76095e12085f
+    - path: output/ashlar/ashlar_output.ome.tif
+      md5sum: fb34bb112d0c95698afa76095e12085f

From f69388794463224ad46dd4c2d1211bf7f6282dd9 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Tue, 16 May 2023 14:29:20 -0400
Subject: [PATCH 069/114] updated docker container URL

---
 modules/nf-core/ashlar/main.nf        | 2 +-
 tests/modules/nf-core/ashlar/test.yml | 3 +++
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index db2e1436d59..013617f6769 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -5,7 +5,7 @@ process ASHLAR {
     conda "bioconda::ashlar=1.17.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ashlar:1.17.0--pyh5e36f6f_0' :
-        'quay.io/biocontainers/ashlar:1.17.0--pyh5e36f6f_0' }"
+        'labsyspharm/ashlar:1.17.0' }"
 
 
     input:
diff --git a/tests/modules/nf-core/ashlar/test.yml b/tests/modules/nf-core/ashlar/test.yml
index 35f837ded1e..6803a937ef0 100644
--- a/tests/modules/nf-core/ashlar/test.yml
+++ b/tests/modules/nf-core/ashlar/test.yml
@@ -5,6 +5,7 @@
   files:
     - path: output/ashlar/ashlar_output.ome.tif
       md5sum: 796fa3687d4ff1389567c22eafb1e4cf
+    - path: output/ashlar/versions.yml
 
 - name: ashlar test_ashlar_all_files
   command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_all_files -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
@@ -13,6 +14,7 @@
   files:
     - path: output/ashlar/ashlar_output.ome.tif
       md5sum: 576bc81fa8d678547e87d25c403ed3a4
+    - path: output/ashlar/versions.yml
 
 - name: ashlar test_ashlar_all_files_tile_size
   command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_all_files_tile_size -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
@@ -21,3 +23,4 @@
   files:
     - path: output/ashlar/ashlar_output.ome.tif
       md5sum: fb34bb112d0c95698afa76095e12085f
+    - path: output/ashlar/versions.yml

From f50061d7ad788daf316061819e212c37236f8195 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Tue, 16 May 2023 14:48:07 -0400
Subject: [PATCH 070/114] testing container URL with hash

---
 modules/nf-core/ashlar/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 013617f6769..e943690f6ed 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -5,7 +5,7 @@ process ASHLAR {
     conda "bioconda::ashlar=1.17.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ashlar:1.17.0--pyh5e36f6f_0' :
-        'labsyspharm/ashlar:1.17.0' }"
+        'labsyspharm/ashlar:1.17.0--pyh5e36f6f_0' }"
 
 
     input:

From b133416aeba89e1b557fe39c7b517e564e27302b Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Tue, 16 May 2023 15:22:26 -0400
Subject: [PATCH 071/114] switched container to docker.io

---
 modules/nf-core/ashlar/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index e943690f6ed..57b9b995284 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -5,7 +5,7 @@ process ASHLAR {
     conda "bioconda::ashlar=1.17.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ashlar:1.17.0--pyh5e36f6f_0' :
-        'labsyspharm/ashlar:1.17.0--pyh5e36f6f_0' }"
+        'docker.io/labsyspharm/ashlar:1.17.0' }"
 
 
     input:

From 3fb1383886bffd906e8ea1cbf004f7e1bd5cd4cf Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Tue, 16 May 2023 17:13:03 -0400
Subject: [PATCH 072/114] fixed meta.yaml lint errors

---
 modules/nf-core/ashlar/meta.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/ashlar/meta.yml b/modules/nf-core/ashlar/meta.yml
index 3fe6f3d3deb..73bb141b865 100644
--- a/modules/nf-core/ashlar/meta.yml
+++ b/modules/nf-core/ashlar/meta.yml
@@ -1,7 +1,9 @@
 name: "ashlar"
 description: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration
 keywords:
-  - image_processing, alignment, registration
+  - image_processing
+  - alignment
+  - registration
 tools:
   #
   - "ashlar":
@@ -19,7 +21,7 @@ input:
         Groovy Map containing sample information
         e.g. [ id:'test', : args: '--flip-x' ]
   - file_in:
-      type: path
+      type: file
       description: multidimentional image data in formats from most commercial microscopes
       pattern: "*.{ome.tiff,ome.tif,rcpnl,btf,nd2,tiff,tif,czi}"
 output:

From fa2e25d3befad69fc443913bd1efb228430030df Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Wed, 17 May 2023 09:59:32 -0400
Subject: [PATCH 073/114] trying CI again with both container hashes

---
 modules/nf-core/ashlar/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 57b9b995284..62811457212 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -5,7 +5,7 @@ process ASHLAR {
     conda "bioconda::ashlar=1.17.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ashlar:1.17.0--pyh5e36f6f_0' :
-        'docker.io/labsyspharm/ashlar:1.17.0' }"
+        'docker.io/labsyspharm/ashlar:1.17.0--pyh5e36f6f_0' }"
 
 
     input:

From f8c84cae2b6277b1e9bf0675293fcb52fc43de5e Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Wed, 17 May 2023 11:28:06 -0400
Subject: [PATCH 074/114] trying with default container registry

---
 modules/nf-core/ashlar/main.nf | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 62811457212..55037b9b7df 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -3,9 +3,7 @@ process ASHLAR {
     label 'process_single'
 
     conda "bioconda::ashlar=1.17.0"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ashlar:1.17.0--pyh5e36f6f_0' :
-        'docker.io/labsyspharm/ashlar:1.17.0--pyh5e36f6f_0' }"
+    container "labsyspharm/ashlar:1.17.0"
 
 
     input:

From efe10c8da955935f8949e350fbf48e62f06af037 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Wed, 17 May 2023 11:33:42 -0400
Subject: [PATCH 075/114] bug fix: removed extra char output in version.yml

---
 modules/nf-core/ashlar/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 55037b9b7df..8e455e96572 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -28,7 +28,7 @@ process ASHLAR {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        ashlar: \$(echo \$(ashlar --version 2>&1) | sed 's/^.*ashlar //; s/Using.*\$//' ))
+        ashlar: \$(echo \$(ashlar --version 2>&1) | sed 's/^.*ashlar //; s/Using.*\$//' )
     END_VERSIONS
     """
 }

From 854865b826d22c2b40fd61ccdbaf789a34ff6455 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Wed, 17 May 2023 15:52:45 -0400
Subject: [PATCH 076/114] changed container URL syntax and it works locally;
 testing with CI

---
 modules/nf-core/ashlar/main.nf | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 8e455e96572..b6b2bff3729 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -2,9 +2,7 @@ process ASHLAR {
     tag '$meta.id'
     label 'process_single'
 
-    conda "bioconda::ashlar=1.17.0"
-    container "labsyspharm/ashlar:1.17.0"
-
+    container "quay.io/biocontainers/ashlar:1.17.0--pyh5e36f6f_0"
 
     input:
     tuple val(meta), path(file_in)

From 9709eb9fcfd9173436890762f9ea7820ce6030bc Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Wed, 17 May 2023 16:04:20 -0400
Subject: [PATCH 077/114] added conda again to test with CI

---
 modules/nf-core/ashlar/main.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index b6b2bff3729..0858fffd903 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -2,6 +2,7 @@ process ASHLAR {
     tag '$meta.id'
     label 'process_single'
 
+    conda "bioconda::ashlar=1.17.0"
     container "quay.io/biocontainers/ashlar:1.17.0--pyh5e36f6f_0"
 
     input:

From 572587203e7a32d1640e9dc83ce096c42470f106 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Thu, 18 May 2023 14:08:45 -0400
Subject: [PATCH 078/114] trying container URL without quay.io again

---
 modules/nf-core/ashlar/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 0858fffd903..c56a96b81c1 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -3,7 +3,7 @@ process ASHLAR {
     label 'process_single'
 
     conda "bioconda::ashlar=1.17.0"
-    container "quay.io/biocontainers/ashlar:1.17.0--pyh5e36f6f_0"
+    container "biocontainers/ashlar:1.17.0--pyh5e36f6f_0"
 
     input:
     tuple val(meta), path(file_in)

From 1bad2c15079a6abd4b9dc7921dbd3e332ac66a46 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Thu, 18 May 2023 16:05:50 -0400
Subject: [PATCH 079/114] testing URL with quay.io again

---
 modules/nf-core/ashlar/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index c56a96b81c1..0858fffd903 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -3,7 +3,7 @@ process ASHLAR {
     label 'process_single'
 
     conda "bioconda::ashlar=1.17.0"
-    container "biocontainers/ashlar:1.17.0--pyh5e36f6f_0"
+    container "quay.io/biocontainers/ashlar:1.17.0--pyh5e36f6f_0"
 
     input:
     tuple val(meta), path(file_in)

From a8e71056a4eeaf1192a0b08f294382b069bb25cd Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Thu, 25 May 2023 11:30:20 -0400
Subject: [PATCH 080/114] added singularity; passes local tests

---
 modules/nf-core/ashlar/main.nf | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 0858fffd903..75d4c5b97e8 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -3,7 +3,9 @@ process ASHLAR {
     label 'process_single'
 
     conda "bioconda::ashlar=1.17.0"
-    container "quay.io/biocontainers/ashlar:1.17.0--pyh5e36f6f_0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ashlar:1.17.0--pyh5e36f6f_0' :
+        'quay.io/biocontainers/ashlar:1.17.0--pyh5e36f6f_0' }"
 
     input:
     tuple val(meta), path(file_in)

From f73e1686a2078dedbcc9712571234a5f3707105a Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Wed, 21 Jun 2023 12:00:08 -0400
Subject: [PATCH 081/114] cleaned-up unused files

---
 modules/nf-core/ashlar/Dockerfile           |  27 ----
 modules/nf-core/ashlar/check_samplesheet.py | 147 --------------------
 modules/nf-core/ashlar/input_check.nf       |  47 -------
 modules/nf-core/ashlar/samplesheet_check.nf |  29 ----
 tests/modules/nf-core/ashlar/test.yml       |   2 +-
 5 files changed, 1 insertion(+), 251 deletions(-)
 delete mode 100644 modules/nf-core/ashlar/Dockerfile
 delete mode 100755 modules/nf-core/ashlar/check_samplesheet.py
 delete mode 100644 modules/nf-core/ashlar/input_check.nf
 delete mode 100644 modules/nf-core/ashlar/samplesheet_check.nf

diff --git a/modules/nf-core/ashlar/Dockerfile b/modules/nf-core/ashlar/Dockerfile
deleted file mode 100644
index b042410b45d..00000000000
--- a/modules/nf-core/ashlar/Dockerfile
+++ /dev/null
@@ -1,27 +0,0 @@
-FROM ubuntu:22.04
-
-RUN apt-get update \
-    && DEBIAN_FRONTEND=noninteractive apt-get install -y \
-        build-essential \
-        ffmpeg \
-        git \
-        openjdk-11-jdk-headless \
-        python3-dev \
-        python3-pip \
-        python3-tk \
-    && rm -rf /var/lib/apt/lists/*
-
-RUN pip3 install -q -U \
-    numpy \
-    pip
-
-COPY / /app/ashlar/
-RUN pip3 install /app/ashlar
-
-ENV OMP_NUM_THREADS 1
-
-VOLUME /data
-VOLUME /data2
-VOLUME /data3
-
-WORKDIR /data
diff --git a/modules/nf-core/ashlar/check_samplesheet.py b/modules/nf-core/ashlar/check_samplesheet.py
deleted file mode 100755
index a7e7b865760..00000000000
--- a/modules/nf-core/ashlar/check_samplesheet.py
+++ /dev/null
@@ -1,147 +0,0 @@
-#!/home/pollen/anaconda3/bin/python3
-
-import os
-import sys
-import errno
-import argparse
-
-
-def parse_args(args=None):
-    Description = "Reformat nf-core/rnaseq samplesheet file and check its contents."
-    Epilog = "Example usage: python check_samplesheet.py <FILE_IN> <FILE_OUT>"
-
-    parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
-    parser.add_argument("FILE_IN", help="Input samplesheet file.")
-    parser.add_argument("FILE_OUT", help="Output file.")
-    return parser.parse_args(args)
-
-
-def make_dir(path):
-    if len(path) > 0:
-        try:
-            os.makedirs(path)
-        except OSError as exception:
-            if exception.errno != errno.EEXIST:
-                raise exception
-
-
-def print_error(error, context="Line", context_str=""):
-    error_str = f"ERROR: Please check samplesheet -> {error}"
-    if context != "" and context_str != "":
-        error_str = f"ERROR: Please check samplesheet -> {error}\n{context.strip()}: '{context_str.strip()}'"
-    print(error_str)
-    sys.exit(1)
-
-
-def check_samplesheet(file_in, file_out):
-    """
-    This function checks that the samplesheet follows the following structure:
-    sample,file_list,args
-    """
-
-    sample_mapping_dict = {}
-    with open(file_in, "r", encoding='utf-8-sig') as fin:
-
-        ## Check header
-        MIN_COLS = 3
-        HEADER = ["sample", "file_list", "args"]
-        header = [x.strip('"') for x in fin.readline().strip().split(",")]
-        if header[: len(HEADER)] != HEADER:
-            print(
-                f"ERROR: Please check samplesheet header -> {','.join(header)} != {','.join(HEADER)}"
-            )
-            sys.exit(1)
-
-        ## Check sample entries
-        for line in fin:
-            if line.strip():
-                lspl = [x.strip().strip('"') for x in line.strip().split(",")]
-
-                ## Check valid number of columns per row
-                if len(lspl) < len(HEADER):
-                    print_error(
-                        f"Invalid number of columns (minimum = {len(HEADER)})!",
-                        "Line",
-                        line,
-                    )
-
-                num_cols = len([x for x in lspl if x])
-                if num_cols < MIN_COLS:
-                    print_error(
-                        f"Invalid number of populated columns (minimum = {MIN_COLS})!",
-                        "Line",
-                        line,
-                    )
-
-                ## Check sample name entries
-                sample, file_list, args = lspl[: len(HEADER)]
-                if sample.find(" ") != -1:
-                    print(
-                        f"WARNING: Spaces have been replaced by underscores for sample: {sample}"
-                    )
-                    sample = sample.replace(" ", "_")
-                if not sample:
-                    print_error("Sample entry has not been specified!", "Line", line)
-
-                ## Check input files
-                if file_list:
-                    print('file_list: {}'.format(file_list))
-                    if file_list.find(" ") != -1:
-                        file_list_list = file_list.split(' ')
-                    else:
-                        file_list_list = [file_list]
-                    print(file_list_list)
-                    for input_file in file_list_list:
-                        print('current input file: {}'.format(input_file))
-                        if not os.path.exists(input_file):
-                            print_error("Input file does not exist!", "Line", line)
-                        if not input_file.endswith(".tiff"):
-                            print_error(
-                                "Input image file must have extension '.tiff' or '.ome.tiff'!",
-                                "Line", line)
-                else:
-                    print_error("Each run must include at least one input image!", "Line", line)
-
-                ## Check optional arguments
-                # TO DO: ashlar will error on bad arguments, so do we need to do any checking here?
-
-                sample_info = [file_list, args]
-                if sample not in sample_mapping_dict:
-                    sample_mapping_dict[sample] = [sample_info]
-                else:
-                    if sample_info in sample_mapping_dict[sample]:
-                        print_error("Samplesheet contains duplicate rows!", "Line", line)
-                    else:
-                        sample_mapping_dict[sample].append(sample_info)
-
-    ## Write validated samplesheet with appropriate columns
-    if len(sample_mapping_dict) > 0:
-        out_dir = os.path.dirname(file_out)
-        make_dir(out_dir)
-        with open(file_out, "w") as fout:
-            fout.write(
-                ",".join(["sample", "file_list", "args"])
-                + "\n"
-            )
-            for sample in sorted(sample_mapping_dict.keys()):
-
-                for idx, val in enumerate(sample_mapping_dict[sample]):
-                    fout.write(",".join([f"{sample}"] + val) + "\n")
-#                    fout.write(",".join([f"{sample}_T{idx+1}"] + val) + "\n")
-    else:
-        print_error(f"No entries to process!", "Samplesheet: {file_in}")
-
-    '''
-    with open(file_in, "r", encoding='utf-8-sig') as fin:
-        with open(file_out, "w") as fout:
-            for line in fin:
-                fout.write(line)
-    '''
-
-def main(args=None):
-    args = parse_args(args)
-    check_samplesheet(args.FILE_IN, args.FILE_OUT)
-
-
-if __name__ == "__main__":
-    sys.exit(main())
diff --git a/modules/nf-core/ashlar/input_check.nf b/modules/nf-core/ashlar/input_check.nf
deleted file mode 100644
index a434135b855..00000000000
--- a/modules/nf-core/ashlar/input_check.nf
+++ /dev/null
@@ -1,47 +0,0 @@
-include { SAMPLESHEET_CHECK } from './samplesheet_check'
-
-workflow INPUT_CHECK {
-
-    println "running INPUT_CHECK..."
-
-    take:
-    samplesheet  // file: ./input_sheet.csv
-
-    main:
-    SAMPLESHEET_CHECK ( samplesheet )
-        .csv
-        .splitCsv (header:true, sep:',')
-        .map { create_image_channel(it) }
-        .view()
-        .set { images }
-
-    emit:
-    images                                     // channel: [ val(meta), path(image) ]
-    versions = SAMPLESHEET_CHECK.out.versions  // channel: [ versions.yml ]
-}
-
-def create_image_channel(LinkedHashMap row) {
-    // create meta map
-    /*
-    def meta = [:]
-    meta.id           = row.sample
-    meta.single_end   = row.single_end.toBoolean()
-    meta.strandedness = row.strandedness
-
-    // add path(s) of the fastq file(s) to the meta map
-    def fastq_meta = []
-    if (!file(row.fastq_1).exists()) {
-        exit 1, "ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!\n${row.fastq_1}"
-    }
-    if (meta.single_end) {
-        fastq_meta = [ meta, [ file(row.fastq_1) ] ]
-    } else {
-        if (!file(row.fastq_2).exists()) {
-            exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}"
-        }
-        fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
-    }
-    return fastq_meta
-    */
-    return row
-}
diff --git a/modules/nf-core/ashlar/samplesheet_check.nf b/modules/nf-core/ashlar/samplesheet_check.nf
deleted file mode 100644
index e709486ab82..00000000000
--- a/modules/nf-core/ashlar/samplesheet_check.nf
+++ /dev/null
@@ -1,29 +0,0 @@
-process SAMPLESHEET_CHECK {
-    tag "$samplesheet"
-
-    conda (params.enable_conda ? "conda-forge::python=3.9.5" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/python:3.9--1' :
-        'quay.io/biocontainers/python:3.9--1' }"
-
-    input:
-    path samplesheet
-
-    output:
-    path '*.csv'       , emit: csv
-    path "versions.yml", emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script: // This script is bundled with the pipeline, in nf-core/rnaseq/bin/
-    """
-    /home/pollen/github/modules/modules/nf-core/ashlar/check_samplesheet.py \\
-        $samplesheet \\
-        samplesheet.valid.csv
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        python: \$(python --version | sed 's/Python //g')
-    END_VERSIONS
-    """
-}
diff --git a/tests/modules/nf-core/ashlar/test.yml b/tests/modules/nf-core/ashlar/test.yml
index 6803a937ef0..96c400d0847 100644
--- a/tests/modules/nf-core/ashlar/test.yml
+++ b/tests/modules/nf-core/ashlar/test.yml
@@ -7,7 +7,7 @@
       md5sum: 796fa3687d4ff1389567c22eafb1e4cf
     - path: output/ashlar/versions.yml
 
-- name: ashlar test_ashlar_all_files
+- name: Sh
   command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_all_files -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
   tags:
     - ashlar

From cd4a50655344af947ee6d37b5d2a98f76d2f6539 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Wed, 21 Jun 2023 12:17:48 -0400
Subject: [PATCH 082/114] removed meta args

---
 modules/nf-core/ashlar/main.nf        |  4 +---
 tests/modules/nf-core/ashlar/main.nf  | 18 ++----------------
 tests/modules/nf-core/ashlar/test.yml | 11 +----------
 3 files changed, 4 insertions(+), 29 deletions(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 75d4c5b97e8..827361a0aa2 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -19,13 +19,11 @@ process ASHLAR {
 
     script:
     def args_conf = task.ext.args ?: ''
-    def args_meta = meta.args ?: ''
 
     """
     ashlar \\
         $file_in \\
-        $args_conf \\
-        $args_meta
+        $args_conf
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index 09630ac97c7..bd1c48cab1b 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -8,7 +8,7 @@ include { ZERO_UUID } from './zero_uuid.nf'
 
 workflow test_ashlar_1_file {
 
-    input_list =  [ [ [ id:'test_all', args: '' ],
+    input_list =  [ [ [ id:'test_all' ],
                [file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle1'], checkIfExists: true)] ] ]
     input_channel = Channel.fromList(input_list)
 
@@ -20,7 +20,7 @@ workflow test_ashlar_1_file {
 
 workflow test_ashlar_all_files {
 
-    input_list =  [ [ [ id:'test_all', args: '' ],
+    input_list =  [ [ [ id:'test_all' ],
                [file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle1'], checkIfExists: true),
                 file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle2'], checkIfExists: true),
                 file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle3'], checkIfExists: true)] ] ]
@@ -31,17 +31,3 @@ workflow test_ashlar_all_files {
     ZERO_UUID ( ASHLAR.out[0], "25169643" )
 
 }
-
-workflow test_ashlar_all_files_tile_size {
-
-    input_list =  [ [ [ id:'test_all', args: '--tile-size 512' ],
-               [file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle1'], checkIfExists: true),
-                file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle2'], checkIfExists: true),
-                file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle3'], checkIfExists: true)] ] ]
-    input_channel = Channel.fromList(input_list)
-
-    ASHLAR ( input_channel )
-
-    ZERO_UUID ( ASHLAR.out[0], "12586923" )
-
-}
diff --git a/tests/modules/nf-core/ashlar/test.yml b/tests/modules/nf-core/ashlar/test.yml
index 96c400d0847..b5ccc9ade76 100644
--- a/tests/modules/nf-core/ashlar/test.yml
+++ b/tests/modules/nf-core/ashlar/test.yml
@@ -7,7 +7,7 @@
       md5sum: 796fa3687d4ff1389567c22eafb1e4cf
     - path: output/ashlar/versions.yml
 
-- name: Sh
+- name: ashlar test_ashlar_all_files
   command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_all_files -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
   tags:
     - ashlar
@@ -15,12 +15,3 @@
     - path: output/ashlar/ashlar_output.ome.tif
       md5sum: 576bc81fa8d678547e87d25c403ed3a4
     - path: output/ashlar/versions.yml
-
-- name: ashlar test_ashlar_all_files_tile_size
-  command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_all_files_tile_size -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
-  tags:
-    - ashlar
-  files:
-    - path: output/ashlar/ashlar_output.ome.tif
-      md5sum: fb34bb112d0c95698afa76095e12085f
-    - path: output/ashlar/versions.yml

From 2e3bd97554792f526cfdd03f727da2c49a8e3cdb Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Wed, 21 Jun 2023 13:40:52 -0400
Subject: [PATCH 083/114] removed unnecessary Channel.toList from test main

---
 tests/modules/nf-core/ashlar/main.nf | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index bd1c48cab1b..5a5c8babeff 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -8,11 +8,10 @@ include { ZERO_UUID } from './zero_uuid.nf'
 
 workflow test_ashlar_1_file {
 
-    input_list =  [ [ [ id:'test_all' ],
-               [file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle1'], checkIfExists: true)] ] ]
-    input_channel = Channel.fromList(input_list)
+    input_list =  [ [ id:'test_all' ],
+               [file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle1'], checkIfExists: true)] ]
 
-    ASHLAR ( input_channel )
+    ASHLAR ( input_list )
 
     ZERO_UUID ( ASHLAR.out[0], "8390123" )
 
@@ -20,13 +19,12 @@ workflow test_ashlar_1_file {
 
 workflow test_ashlar_all_files {
 
-    input_list =  [ [ [ id:'test_all' ],
+    input_list =  [ [ id:'test_all' ],
                [file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle1'], checkIfExists: true),
                 file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle2'], checkIfExists: true),
-                file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle3'], checkIfExists: true)] ] ]
-    input_channel = Channel.fromList(input_list)
+                file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle3'], checkIfExists: true)] ]
 
-    ASHLAR ( input_channel )
+    ASHLAR ( input_list )
 
     ZERO_UUID ( ASHLAR.out[0], "25169643" )
 

From 27a0c1d87dc202c01dc9dccc9cf39d9589601488 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Wed, 21 Jun 2023 14:22:47 -0400
Subject: [PATCH 084/114] restored tile test using withName technique for param

---
 tests/modules/nf-core/ashlar/main.nf         | 15 +++++++++++++++
 tests/modules/nf-core/ashlar/nextflow.config |  4 +++-
 tests/modules/nf-core/ashlar/test.yml        |  9 +++++++++
 3 files changed, 27 insertions(+), 1 deletion(-)

diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index 5a5c8babeff..bd99b1b7b50 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -3,6 +3,8 @@
 nextflow.enable.dsl = 2
 
 include { ASHLAR } from '../../../../modules/nf-core/ashlar/main.nf'
+include { ASHLAR as ASHLAR_TILE } from '../../../../modules/nf-core/ashlar/main.nf'
+
 // we zero out the UUID of output tiff images with ZERO_UUID so we get a consistent md5sum
 include { ZERO_UUID } from './zero_uuid.nf'
 
@@ -29,3 +31,16 @@ workflow test_ashlar_all_files {
     ZERO_UUID ( ASHLAR.out[0], "25169643" )
 
 }
+
+workflow test_ashlar_all_files_tile_size {
+
+    input_list =  [ [ id:'test_all' ],
+               [file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle1'], checkIfExists: true),
+                file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle2'], checkIfExists: true),
+                file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle3'], checkIfExists: true)] ]
+
+    ASHLAR_TILE ( input_list )
+
+    ZERO_UUID ( ASHLAR_TILE.out[0], "12586923" )
+
+}
diff --git a/tests/modules/nf-core/ashlar/nextflow.config b/tests/modules/nf-core/ashlar/nextflow.config
index 2f39c310f4c..9b566dd3953 100644
--- a/tests/modules/nf-core/ashlar/nextflow.config
+++ b/tests/modules/nf-core/ashlar/nextflow.config
@@ -2,6 +2,8 @@ process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
-    ext.args = ""
+    withName: ASHLAR_TILE {
+        ext.args = "--tile-size 512"
+    }
 
 }
diff --git a/tests/modules/nf-core/ashlar/test.yml b/tests/modules/nf-core/ashlar/test.yml
index b5ccc9ade76..6803a937ef0 100644
--- a/tests/modules/nf-core/ashlar/test.yml
+++ b/tests/modules/nf-core/ashlar/test.yml
@@ -15,3 +15,12 @@
     - path: output/ashlar/ashlar_output.ome.tif
       md5sum: 576bc81fa8d678547e87d25c403ed3a4
     - path: output/ashlar/versions.yml
+
+- name: ashlar test_ashlar_all_files_tile_size
+  command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_all_files_tile_size -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
+  tags:
+    - ashlar
+  files:
+    - path: output/ashlar/ashlar_output.ome.tif
+      md5sum: fb34bb112d0c95698afa76095e12085f
+    - path: output/ashlar/versions.yml

From 19ec447b42995cbf5946abb8ebe6dda3098d8157 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Wed, 21 Jun 2023 14:49:03 -0400
Subject: [PATCH 085/114] simplified input arg name

---
 modules/nf-core/ashlar/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 827361a0aa2..c82ea13595b 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -18,12 +18,12 @@ process ASHLAR {
     task.ext.when == null || task.ext.when
 
     script:
-    def args_conf = task.ext.args ?: ''
+    def args = task.ext.args ?: ''
 
     """
     ashlar \\
         $file_in \\
-        $args_conf
+        $args
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From a2a5c967babd986a499c03bb1e7b496af428bed0 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Wed, 21 Jun 2023 14:58:37 -0400
Subject: [PATCH 086/114] updated module output path and emit

---
 modules/nf-core/ashlar/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index c82ea13595b..5c56a625808 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -11,8 +11,8 @@ process ASHLAR {
     tuple val(meta), path(file_in)
 
     output:
-    tuple val(meta), path("*.tif")      ,   emit: ashlar_tif
-    path "versions.yml"                 ,   emit: versions
+    tuple val(meta), path("*.ome.tif")      ,   emit: tif
+    path "versions.yml"                     ,   emit: versions
 
     when:
     task.ext.when == null || task.ext.when

From 352d5793d2ee56a2e36968f227075a8ccbbf4c26 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Wed, 21 Jun 2023 15:06:00 -0400
Subject: [PATCH 087/114] updated module usage command

---
 modules/nf-core/ashlar/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 5c56a625808..520286af4a5 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -27,7 +27,7 @@ process ASHLAR {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        ashlar: \$(echo \$(ashlar --version 2>&1) | sed 's/^.*ashlar //; s/Using.*\$//' )
+        ashlar: \$(ashlar --version 2>&1 | sed 's/^.*ashlar //; s/Using.*\$//' )
     END_VERSIONS
     """
 }

From ff0ef63f7b4d8e9fe996f1cdc61dc64428ecae64 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Wed, 21 Jun 2023 15:13:36 -0400
Subject: [PATCH 088/114] updated licence in meta

---
 modules/nf-core/ashlar/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/ashlar/meta.yml b/modules/nf-core/ashlar/meta.yml
index 73bb141b865..dd02c2738b3 100644
--- a/modules/nf-core/ashlar/meta.yml
+++ b/modules/nf-core/ashlar/meta.yml
@@ -11,7 +11,7 @@ tools:
       homepage: "https://labsyspharm.github.io/ashlar/"
       documentation: "https://labsyspharm.github.io/ashlar/"
       doi: "10.1093/bioinformatics/btac544"
-      licence: "['MIT']"
+      licence: ["MIT"]
 
 input:
   #

From 97c5bebbf519224c7ad4292ce3763ef2eb403e48 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Wed, 21 Jun 2023 15:31:44 -0400
Subject: [PATCH 089/114] cleaned-up meta.yml

---
 modules/nf-core/ashlar/meta.yml | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/modules/nf-core/ashlar/meta.yml b/modules/nf-core/ashlar/meta.yml
index dd02c2738b3..a2207ec8d9f 100644
--- a/modules/nf-core/ashlar/meta.yml
+++ b/modules/nf-core/ashlar/meta.yml
@@ -5,7 +5,6 @@ keywords:
   - alignment
   - registration
 tools:
-  #
   - "ashlar":
       description: "Alignment by Simultaneous Harmonization of Layer/Adjacency Registration"
       homepage: "https://labsyspharm.github.io/ashlar/"
@@ -14,24 +13,22 @@ tools:
       licence: ["MIT"]
 
 input:
-  #
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
-        e.g. [ id:'test', : args: '--flip-x' ]
+        e.g. [ id:'test' ]
   - file_in:
       type: file
-      description: multidimentional image data in formats from most commercial microscopes
+      description: Overlapping tile image data in formats from most commercial microscopes
       pattern: "*.{ome.tiff,ome.tif,rcpnl,btf,nd2,tiff,tif,czi}"
 output:
-  #
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
-        e.g. [ id:'test', : args: '--flip-x' ]
-  - file_out:
+        e.g. [ id:'test' ]
+  - tif:
       type: file
       description: pyramidal OME-TIFF
       pattern: "*.ome.tif"

From c8bdccd36194ef0eb6f137884a0f8939cdd769d8 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Thu, 22 Jun 2023 15:24:11 -0400
Subject: [PATCH 090/114] Update modules/nf-core/ashlar/main.nf

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
---
 modules/nf-core/ashlar/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 520286af4a5..a98699ed7e6 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -5,7 +5,7 @@ process ASHLAR {
     conda "bioconda::ashlar=1.17.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ashlar:1.17.0--pyh5e36f6f_0' :
-        'quay.io/biocontainers/ashlar:1.17.0--pyh5e36f6f_0' }"
+        'biocontainers/ashlar:1.17.0--pyh5e36f6f_0' }"
 
     input:
     tuple val(meta), path(file_in)

From c1f36ae52858da776b9fa8b0a8ea2c000d1d7147 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Thu, 22 Jun 2023 15:28:32 -0400
Subject: [PATCH 091/114] Update modules/nf-core/ashlar/main.nf

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
---
 modules/nf-core/ashlar/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index a98699ed7e6..9296c728bbc 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -12,7 +12,7 @@ process ASHLAR {
 
     output:
     tuple val(meta), path("*.ome.tif")      ,   emit: tif
-    path "versions.yml"                     ,   emit: versions
+    path "versions.yml"                , emit: versions
 
     when:
     task.ext.when == null || task.ext.when

From 9b018f27c9b8ad29e878235b983c1850341e3a16 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Thu, 22 Jun 2023 15:28:41 -0400
Subject: [PATCH 092/114] Update modules/nf-core/ashlar/main.nf

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
---
 modules/nf-core/ashlar/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 9296c728bbc..c522872c620 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -11,7 +11,7 @@ process ASHLAR {
     tuple val(meta), path(file_in)
 
     output:
-    tuple val(meta), path("*.ome.tif")      ,   emit: tif
+    tuple val(meta), path("*.ome.tif"), emit: tif
     path "versions.yml"                , emit: versions
 
     when:

From cc5c66878902e821bc60b7a4aedfb71cd7918e63 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Thu, 22 Jun 2023 16:48:57 -0400
Subject: [PATCH 093/114] changed dfp and ffp to optional input channels and
 tested with no input files

---
 modules/nf-core/ashlar/main.nf       | 14 ++++++++++----
 tests/modules/nf-core/ashlar/main.nf |  6 +++---
 2 files changed, 13 insertions(+), 7 deletions(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index c522872c620..1dc33cfde41 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -8,22 +8,28 @@ process ASHLAR {
         'biocontainers/ashlar:1.17.0--pyh5e36f6f_0' }"
 
     input:
-    tuple val(meta), path(file_in)
+    tuple val(meta), path(file)
+    path(opt_dfp)
+    path(opt_ffp)
 
     output:
     tuple val(meta), path("*.ome.tif"), emit: tif
-    path "versions.yml"                , emit: versions
+    path "versions.yml"               , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
+    def dfp = opt_dfp? "--dfp $opt_dfp": ""
+    def ffp = opt_ffp? "--dfp $opt_ffp": ""
 
     """
     ashlar \\
-        $file_in \\
-        $args
+        $file \\
+        $args \\
+        $dfp \\
+        $ffp
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index bd99b1b7b50..1a062d298a6 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -13,7 +13,7 @@ workflow test_ashlar_1_file {
     input_list =  [ [ id:'test_all' ],
                [file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle1'], checkIfExists: true)] ]
 
-    ASHLAR ( input_list )
+    ASHLAR ( input_list, [], [] )
 
     ZERO_UUID ( ASHLAR.out[0], "8390123" )
 
@@ -26,7 +26,7 @@ workflow test_ashlar_all_files {
                 file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle2'], checkIfExists: true),
                 file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle3'], checkIfExists: true)] ]
 
-    ASHLAR ( input_list )
+    ASHLAR ( input_list, [], [] )
 
     ZERO_UUID ( ASHLAR.out[0], "25169643" )
 
@@ -39,7 +39,7 @@ workflow test_ashlar_all_files_tile_size {
                 file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle2'], checkIfExists: true),
                 file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle3'], checkIfExists: true)] ]
 
-    ASHLAR_TILE ( input_list )
+    ASHLAR_TILE ( input_list, [], [] )
 
     ZERO_UUID ( ASHLAR_TILE.out[0], "12586923" )
 

From 1e03f60a6d33e973d429f4ae45ce2a5f037b4c3f Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Fri, 23 Jun 2023 12:03:31 -0400
Subject: [PATCH 094/114] added dfp ffp test with hard-coded files

---
 modules/nf-core/ashlar/main.nf        |  2 +-
 tests/modules/nf-core/ashlar/main.nf  | 13 +++++++++++++
 tests/modules/nf-core/ashlar/test.yml |  9 +++++++++
 3 files changed, 23 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 1dc33cfde41..178824bd5bb 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -22,7 +22,7 @@ process ASHLAR {
     script:
     def args = task.ext.args ?: ''
     def dfp = opt_dfp? "--dfp $opt_dfp": ""
-    def ffp = opt_ffp? "--dfp $opt_ffp": ""
+    def ffp = opt_ffp? "--ffp $opt_ffp": ""
 
     """
     ashlar \\
diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index 1a062d298a6..8b2f8cde3a9 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -44,3 +44,16 @@ workflow test_ashlar_all_files_tile_size {
     ZERO_UUID ( ASHLAR_TILE.out[0], "12586923" )
 
 }
+
+workflow test_ashlar_1_file_dfp_ffp {
+
+    input_list =  [ [ id:'test_all' ],
+               [file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle1'], checkIfExists: true)] ]
+
+    ASHLAR ( input_list, file('./cycif-tonsil-small-dfp.tif', checkIfExists: true),
+                         file('./cycif-tonsil-small-ffp.tif', checkIfExists: true) )
+
+    ZERO_UUID ( ASHLAR.out[0], "8390123" )
+
+}
+
diff --git a/tests/modules/nf-core/ashlar/test.yml b/tests/modules/nf-core/ashlar/test.yml
index 6803a937ef0..aac024156d8 100644
--- a/tests/modules/nf-core/ashlar/test.yml
+++ b/tests/modules/nf-core/ashlar/test.yml
@@ -24,3 +24,12 @@
     - path: output/ashlar/ashlar_output.ome.tif
       md5sum: fb34bb112d0c95698afa76095e12085f
     - path: output/ashlar/versions.yml
+
+- name: ashlar test_ashlar_1_file_dfp_ffp
+  command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_1_file_dfp_ffp -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
+  tags:
+    - ashlar
+  files:
+    - path: output/ashlar/ashlar_output.ome.tif
+      md5sum: 796fa3687d4ff1389567c22eafb1e4cf
+    - path: output/ashlar/versions.yml

From 3a5e027147c1f742c25e554a77c279752bd3f050 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Mon, 26 Jun 2023 15:39:10 -0400
Subject: [PATCH 095/114] added validation for dfp and ffp

---
 modules/nf-core/ashlar/main.nf       | 12 ++++++++++++
 tests/modules/nf-core/ashlar/main.nf |  4 ++--
 2 files changed, 14 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 178824bd5bb..b4f2cf4b48e 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -23,8 +23,20 @@ process ASHLAR {
     def args = task.ext.args ?: ''
     def dfp = opt_dfp? "--dfp $opt_dfp": ""
     def ffp = opt_ffp? "--ffp $opt_ffp": ""
+    def dfp_validated = !(opt_dfp instanceof List) || ((opt_dfp instanceof List) && (opt_dfp.isEmpty() || opt_dfp.size() == 1)) ? true : false
+    def ffp_validated = !(opt_ffp instanceof List) || ((opt_ffp instanceof List) && (opt_ffp.isEmpty() || opt_ffp.size() == 1)) ? true : false
 
     """
+    if [ "$dfp_validated" = "false" ]; then
+        echo "Error: please input only zero or one dfp files"
+        exit 1
+    fi
+
+    if [ "$ffp_validated" = "false" ]; then
+        echo "Error: please input only zero or one ffp files"
+        exit 1
+    fi
+
     ashlar \\
         $file \\
         $args \\
diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index 8b2f8cde3a9..321ef7ee140 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -50,8 +50,8 @@ workflow test_ashlar_1_file_dfp_ffp {
     input_list =  [ [ id:'test_all' ],
                [file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle1'], checkIfExists: true)] ]
 
-    ASHLAR ( input_list, file('./cycif-tonsil-small-dfp.tif', checkIfExists: true),
-                         file('./cycif-tonsil-small-ffp.tif', checkIfExists: true) )
+    ASHLAR ( input_list, [file('./cycif-tonsil-small-dfp.tif', checkIfExists: true)],
+                         [file('./cycif-tonsil-small-ffp.tif', checkIfExists: true)] )
 
     ZERO_UUID ( ASHLAR.out[0], "8390123" )
 

From b746eead10f3967ea83fe93ffb62377fdf66f00d Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Wed, 28 Jun 2023 16:47:14 -0400
Subject: [PATCH 096/114] changed validation for dfp/ffp and added test

---
 modules/nf-core/ashlar/main.nf        | 11 +++++++----
 tests/modules/nf-core/ashlar/main.nf  | 15 +++++++++++++++
 tests/modules/nf-core/ashlar/test.yml |  9 +++++++++
 3 files changed, 31 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index b4f2cf4b48e..1f72438bc39 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -21,10 +21,13 @@ process ASHLAR {
 
     script:
     def args = task.ext.args ?: ''
-    def dfp = opt_dfp? "--dfp $opt_dfp": ""
-    def ffp = opt_ffp? "--ffp $opt_ffp": ""
-    def dfp_validated = !(opt_dfp instanceof List) || ((opt_dfp instanceof List) && (opt_dfp.isEmpty() || opt_dfp.size() == 1)) ? true : false
-    def ffp_validated = !(opt_ffp instanceof List) || ((opt_ffp instanceof List) && (opt_ffp.isEmpty() || opt_ffp.size() == 1)) ? true : false
+    def dfp = opt_dfp ? "--dfp $opt_dfp" : ""
+    def ffp = opt_ffp ? "--ffp $opt_ffp" : ""
+    def num_files = file instanceof List ? file.size() : 1
+    def opt_dfp_size = opt_dfp instanceof List ? opt_dfp.size() : 1
+    def opt_ffp_size = opt_ffp instanceof List ? opt_ffp.size() : 1
+    def dfp_validated = (opt_dfp_size == 0 || opt_dfp_size == 1 || opt_dfp_size == num_files) ? true : false
+    def ffp_validated = (opt_ffp_size == 0 || opt_ffp_size == 1 || opt_ffp_size == num_files) ? true : false
 
     """
     if [ "$dfp_validated" = "false" ]; then
diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index 321ef7ee140..5fbaf603ed9 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -45,6 +45,21 @@ workflow test_ashlar_all_files_tile_size {
 
 }
 
+workflow test_ashlar_all_files_dfp_ffp {
+
+    input_list =  [ [ id:'test_all' ],
+               [file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle1'], checkIfExists: true),
+                file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle2'], checkIfExists: true),
+                file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle3'], checkIfExists: true)] ]
+
+    ASHLAR ( input_list, [file('./cycif-tonsil-small-dfp.tif', checkIfExists: true)],
+                         [file('./cycif-tonsil-small-ffp.tif', checkIfExists: true)] )
+
+
+    ZERO_UUID ( ASHLAR.out[0], "25169643" )
+
+}
+
 workflow test_ashlar_1_file_dfp_ffp {
 
     input_list =  [ [ id:'test_all' ],
diff --git a/tests/modules/nf-core/ashlar/test.yml b/tests/modules/nf-core/ashlar/test.yml
index aac024156d8..21315a5f025 100644
--- a/tests/modules/nf-core/ashlar/test.yml
+++ b/tests/modules/nf-core/ashlar/test.yml
@@ -25,6 +25,15 @@
       md5sum: fb34bb112d0c95698afa76095e12085f
     - path: output/ashlar/versions.yml
 
+- name: ashlar test_ashlar_all_files_dfp_ffp
+  command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_all_files_dfp_ffp -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
+  tags:
+    - ashlar
+  files:
+    - path: output/ashlar/ashlar_output.ome.tif
+      md5sum: 576bc81fa8d678547e87d25c403ed3a4
+    - path: output/ashlar/versions.yml
+
 - name: ashlar test_ashlar_1_file_dfp_ffp
   command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_1_file_dfp_ffp -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
   tags:

From e9d0b1905087fc7dafebd0dfbf4f2c9d81d42d35 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Mon, 24 Jul 2023 14:05:52 -0400
Subject: [PATCH 097/114] now pulling dfp/ffp from test_data repo

---
 tests/config/test_data.config         | 2 ++
 tests/modules/nf-core/ashlar/main.nf  | 9 ++++-----
 tests/modules/nf-core/ashlar/test.yml | 2 +-
 3 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index b45ee031192..5933bdbaf79 100644
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@@ -669,6 +669,8 @@ params {
                 cycif_tonsil_cycle1     = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif"
                 cycif_tonsil_cycle2     = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-cycle2.ome.tif"
                 cycif_tonsil_cycle3     = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-cycle3.ome.tif"
+                cycif_tonsil_dfp        = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-dfp.ome.tif"
+                cycif_tonsil_ffp        = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-ffp.ome.tif"
             }
             'registration' {
                 markers                 = "${params.test_data_base}/data/imaging/registration/markers.csv"
diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index 5fbaf603ed9..baab24f75b7 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -52,9 +52,8 @@ workflow test_ashlar_all_files_dfp_ffp {
                 file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle2'], checkIfExists: true),
                 file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle3'], checkIfExists: true)] ]
 
-    ASHLAR ( input_list, [file('./cycif-tonsil-small-dfp.tif', checkIfExists: true)],
-                         [file('./cycif-tonsil-small-ffp.tif', checkIfExists: true)] )
-
+    ASHLAR ( input_list, [file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_dfp'], checkIfExists: true)],
+                         [file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_ffp'], checkIfExists: true)] )
 
     ZERO_UUID ( ASHLAR.out[0], "25169643" )
 
@@ -65,8 +64,8 @@ workflow test_ashlar_1_file_dfp_ffp {
     input_list =  [ [ id:'test_all' ],
                [file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle1'], checkIfExists: true)] ]
 
-    ASHLAR ( input_list, [file('./cycif-tonsil-small-dfp.tif', checkIfExists: true)],
-                         [file('./cycif-tonsil-small-ffp.tif', checkIfExists: true)] )
+    ASHLAR ( input_list, [file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_dfp'], checkIfExists: true)],
+                         [file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_ffp'], checkIfExists: true)] )
 
     ZERO_UUID ( ASHLAR.out[0], "8390123" )
 
diff --git a/tests/modules/nf-core/ashlar/test.yml b/tests/modules/nf-core/ashlar/test.yml
index 21315a5f025..7e851355255 100644
--- a/tests/modules/nf-core/ashlar/test.yml
+++ b/tests/modules/nf-core/ashlar/test.yml
@@ -1,5 +1,5 @@
 - name: ashlar test_ashlar_1_file
-  command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_1_file -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
+  command: nextflow run -entry test_ashlar_1_file -plugins nf-validation tests/modules/nf-core/ashlar/main.nf -c tests/config/nextflow.config --input /home/pollen/github/modules/tests/modules/nf-core/ashlar/test_sheet_url.csv
   tags:
     - ashlar
   files:

From 6e192d76e83baa5d39be4b1c10a3dfe351810d48 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Mon, 31 Jul 2023 14:20:42 -0400
Subject: [PATCH 098/114] test_data formatting change

---
 tests/modules/nf-core/ashlar/main.nf | 64 ++++++++++++++++++++--------
 1 file changed, 47 insertions(+), 17 deletions(-)

diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index baab24f75b7..42819a7a91d 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -11,7 +11,9 @@ include { ZERO_UUID } from './zero_uuid.nf'
 workflow test_ashlar_1_file {
 
     input_list =  [ [ id:'test_all' ],
-               [file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle1'], checkIfExists: true)] ]
+               [file(params.test_data['imaging']
+                                     ['ome-tiff']
+                                     ['cycif_tonsil_cycle1'], checkIfExists: true)] ]
 
     ASHLAR ( input_list, [], [] )
 
@@ -22,9 +24,15 @@ workflow test_ashlar_1_file {
 workflow test_ashlar_all_files {
 
     input_list =  [ [ id:'test_all' ],
-               [file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle1'], checkIfExists: true),
-                file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle2'], checkIfExists: true),
-                file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle3'], checkIfExists: true)] ]
+               [file(params.test_data['imaging']
+                                     ['ome-tiff']
+                                     ['cycif_tonsil_cycle1'], checkIfExists: true),
+                file(params.test_data['imaging']
+                                     ['ome-tiff']
+                                     ['cycif_tonsil_cycle2'], checkIfExists: true),
+                file(params.test_data['imaging']
+                                     ['ome-tiff']
+                                     ['cycif_tonsil_cycle3'], checkIfExists: true)] ]
 
     ASHLAR ( input_list, [], [] )
 
@@ -35,9 +43,15 @@ workflow test_ashlar_all_files {
 workflow test_ashlar_all_files_tile_size {
 
     input_list =  [ [ id:'test_all' ],
-               [file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle1'], checkIfExists: true),
-                file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle2'], checkIfExists: true),
-                file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle3'], checkIfExists: true)] ]
+               [file(params.test_data['imaging']
+                                     ['ome-tiff']
+                                     ['cycif_tonsil_cycle1'], checkIfExists: true),
+                file(params.test_data['imaging']
+                                     ['ome-tiff']
+                                     ['cycif_tonsil_cycle2'], checkIfExists: true),
+                file(params.test_data['imaging']
+                                     ['ome-tiff']
+                                     ['cycif_tonsil_cycle3'], checkIfExists: true)] ]
 
     ASHLAR_TILE ( input_list, [], [] )
 
@@ -48,12 +62,22 @@ workflow test_ashlar_all_files_tile_size {
 workflow test_ashlar_all_files_dfp_ffp {
 
     input_list =  [ [ id:'test_all' ],
-               [file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle1'], checkIfExists: true),
-                file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle2'], checkIfExists: true),
-                file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle3'], checkIfExists: true)] ]
-
-    ASHLAR ( input_list, [file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_dfp'], checkIfExists: true)],
-                         [file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_ffp'], checkIfExists: true)] )
+               [file(params.test_data['imaging']
+                                     ['ome-tiff']
+                                     ['cycif_tonsil_cycle1'], checkIfExists: true),
+                file(params.test_data['imaging']
+                                     ['ome-tiff']
+                                     ['cycif_tonsil_cycle2'], checkIfExists: true),
+                file(params.test_data['imaging']
+                                     ['ome-tiff']
+                                     ['cycif_tonsil_cycle3'], checkIfExists: true)] ]
+
+    ASHLAR ( input_list, [file(params.test_data['imaging']
+                                               ['ome-tiff']
+                                               ['cycif_tonsil_dfp'], checkIfExists: true)],
+                         [file(params.test_data['imaging']
+                                               ['ome-tiff']
+                                               ['cycif_tonsil_ffp'], checkIfExists: true)] )
 
     ZERO_UUID ( ASHLAR.out[0], "25169643" )
 
@@ -62,10 +86,16 @@ workflow test_ashlar_all_files_dfp_ffp {
 workflow test_ashlar_1_file_dfp_ffp {
 
     input_list =  [ [ id:'test_all' ],
-               [file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_cycle1'], checkIfExists: true)] ]
-
-    ASHLAR ( input_list, [file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_dfp'], checkIfExists: true)],
-                         [file(params.test_data['imaging']['ome-tiff']['cycif_tonsil_ffp'], checkIfExists: true)] )
+               [file(params.test_data['imaging']
+                                     ['ome-tiff']
+                                     ['cycif_tonsil_cycle1'], checkIfExists: true)] ]
+
+    ASHLAR ( input_list, [file(params.test_data['imaging']
+                                               ['ome-tiff']
+                                               ['cycif_tonsil_dfp'], checkIfExists: true)],
+                         [file(params.test_data['imaging']
+                                               ['ome-tiff']
+                                               ['cycif_tonsil_ffp'], checkIfExists: true)] )
 
     ZERO_UUID ( ASHLAR.out[0], "8390123" )
 

From e660f936b75e1ed66dd0bc9ae895db88cdad5bb5 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Thu, 3 Aug 2023 10:20:31 -0400
Subject: [PATCH 099/114] Update modules/nf-core/ashlar/main.nf

moved dfp/ffp validation into script block

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
---
 modules/nf-core/ashlar/main.nf | 11 ++---------
 1 file changed, 2 insertions(+), 9 deletions(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 1f72438bc39..65c36a745c9 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -29,16 +29,9 @@ process ASHLAR {
     def dfp_validated = (opt_dfp_size == 0 || opt_dfp_size == 1 || opt_dfp_size == num_files) ? true : false
     def ffp_validated = (opt_ffp_size == 0 || opt_ffp_size == 1 || opt_ffp_size == num_files) ? true : false
 
+    if ( !dfp_validated ) { error "Please input only zero or one dfp files" }
+    if ( !ffp_validated ) { error "Please input only zero or one ffp files" }
     """
-    if [ "$dfp_validated" = "false" ]; then
-        echo "Error: please input only zero or one dfp files"
-        exit 1
-    fi
-
-    if [ "$ffp_validated" = "false" ]; then
-        echo "Error: please input only zero or one ffp files"
-        exit 1
-    fi
 
     ashlar \\
         $file \\

From 6d7fa19f223b2d2f026c7ed767b996a4fb9e9454 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Thu, 3 Aug 2023 10:47:48 -0400
Subject: [PATCH 100/114] corrected dfp/ffp error message

---
 modules/nf-core/ashlar/main.nf | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 65c36a745c9..9e947f36164 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -29,8 +29,9 @@ process ASHLAR {
     def dfp_validated = (opt_dfp_size == 0 || opt_dfp_size == 1 || opt_dfp_size == num_files) ? true : false
     def ffp_validated = (opt_ffp_size == 0 || opt_ffp_size == 1 || opt_ffp_size == num_files) ? true : false
 
-    if ( !dfp_validated ) { error "Please input only zero or one dfp files" }
-    if ( !ffp_validated ) { error "Please input only zero or one ffp files" }
+    if ( !dfp_validated ) { error "Please input only zero, one, or N dfp files, where N is the number of input images" }
+    if ( !ffp_validated ) { error "Please input only zero, one, or N ffp files, where N is the number of input images" }
+
     """
 
     ashlar \\

From 059c947a30c6fcae7d61f54f60c75ea9f1f446a5 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Thu, 3 Aug 2023 11:37:59 -0400
Subject: [PATCH 101/114] Update modules/nf-core/ashlar/meta.yml

corrected input name

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
---
 modules/nf-core/ashlar/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/ashlar/meta.yml b/modules/nf-core/ashlar/meta.yml
index a2207ec8d9f..f721f34ad6b 100644
--- a/modules/nf-core/ashlar/meta.yml
+++ b/modules/nf-core/ashlar/meta.yml
@@ -18,7 +18,7 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test' ]
-  - file_in:
+  - file:
       type: file
       description: Overlapping tile image data in formats from most commercial microscopes
       pattern: "*.{ome.tiff,ome.tif,rcpnl,btf,nd2,tiff,tif,czi}"

From 3b26a84e3aa38f7b40070615e420c1804ec4ddcb Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Thu, 3 Aug 2023 11:39:18 -0400
Subject: [PATCH 102/114] Update modules/nf-core/ashlar/meta.yml

made file description more informative

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
---
 modules/nf-core/ashlar/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/ashlar/meta.yml b/modules/nf-core/ashlar/meta.yml
index f721f34ad6b..682caa7dee9 100644
--- a/modules/nf-core/ashlar/meta.yml
+++ b/modules/nf-core/ashlar/meta.yml
@@ -30,7 +30,7 @@ output:
         e.g. [ id:'test' ]
   - tif:
       type: file
-      description: pyramidal OME-TIFF
+      description: A pyramidal, tiled OME-TIFF file created from input images.
       pattern: "*.ome.tif"
   - versions:
       type: file

From 65f2e98c317831c3ed066cbbe4fe40f87262c51d Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Thu, 3 Aug 2023 11:56:08 -0400
Subject: [PATCH 103/114] finished input name change

---
 modules/nf-core/ashlar/main.nf  | 6 +++---
 modules/nf-core/ashlar/meta.yml | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 9e947f36164..79e4d2ce172 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -8,7 +8,7 @@ process ASHLAR {
         'biocontainers/ashlar:1.17.0--pyh5e36f6f_0' }"
 
     input:
-    tuple val(meta), path(file)
+    tuple val(meta), path(images)
     path(opt_dfp)
     path(opt_ffp)
 
@@ -23,7 +23,7 @@ process ASHLAR {
     def args = task.ext.args ?: ''
     def dfp = opt_dfp ? "--dfp $opt_dfp" : ""
     def ffp = opt_ffp ? "--ffp $opt_ffp" : ""
-    def num_files = file instanceof List ? file.size() : 1
+    def num_files = images instanceof List ? images.size() : 1
     def opt_dfp_size = opt_dfp instanceof List ? opt_dfp.size() : 1
     def opt_ffp_size = opt_ffp instanceof List ? opt_ffp.size() : 1
     def dfp_validated = (opt_dfp_size == 0 || opt_dfp_size == 1 || opt_dfp_size == num_files) ? true : false
@@ -35,7 +35,7 @@ process ASHLAR {
     """
 
     ashlar \\
-        $file \\
+        $images \\
         $args \\
         $dfp \\
         $ffp
diff --git a/modules/nf-core/ashlar/meta.yml b/modules/nf-core/ashlar/meta.yml
index 682caa7dee9..244e9726616 100644
--- a/modules/nf-core/ashlar/meta.yml
+++ b/modules/nf-core/ashlar/meta.yml
@@ -18,7 +18,7 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test' ]
-  - file:
+  - images:
       type: file
       description: Overlapping tile image data in formats from most commercial microscopes
       pattern: "*.{ome.tiff,ome.tif,rcpnl,btf,nd2,tiff,tif,czi}"

From 0e5e56baa69cb1464ef924bbcb5b79260abb128f Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Thu, 3 Aug 2023 14:48:31 -0400
Subject: [PATCH 104/114] Apply suggestions from code review

nice, I didn't realize it could be referenced like that. Thanks!

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
---
 tests/modules/nf-core/ashlar/main.nf | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index 42819a7a91d..942e44deb4b 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -17,7 +17,7 @@ workflow test_ashlar_1_file {
 
     ASHLAR ( input_list, [], [] )
 
-    ZERO_UUID ( ASHLAR.out[0], "8390123" )
+    ZERO_UUID ( ASHLAR.out.tif, "8390123" )
 
 }
 
@@ -36,7 +36,7 @@ workflow test_ashlar_all_files {
 
     ASHLAR ( input_list, [], [] )
 
-    ZERO_UUID ( ASHLAR.out[0], "25169643" )
+    ZERO_UUID ( ASHLAR.out.tif, "25169643" )
 
 }
 
@@ -55,7 +55,7 @@ workflow test_ashlar_all_files_tile_size {
 
     ASHLAR_TILE ( input_list, [], [] )
 
-    ZERO_UUID ( ASHLAR_TILE.out[0], "12586923" )
+    ZERO_UUID ( ASHLAR_TILE.out.tif, "12586923" )
 
 }
 
@@ -79,7 +79,7 @@ workflow test_ashlar_all_files_dfp_ffp {
                                                ['ome-tiff']
                                                ['cycif_tonsil_ffp'], checkIfExists: true)] )
 
-    ZERO_UUID ( ASHLAR.out[0], "25169643" )
+    ZERO_UUID ( ASHLAR.out.tif, "25169643" )
 
 }
 
@@ -97,7 +97,7 @@ workflow test_ashlar_1_file_dfp_ffp {
                                                ['ome-tiff']
                                                ['cycif_tonsil_ffp'], checkIfExists: true)] )
 
-    ZERO_UUID ( ASHLAR.out[0], "8390123" )
+    ZERO_UUID ( ASHLAR.out.tif, "8390123" )
 
 }
 

From 8bec89df5dc2f8ae962c70571f8d50541cf45601 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Thu, 3 Aug 2023 15:12:34 -0400
Subject: [PATCH 105/114] Update tests/modules/nf-core/ashlar/main.nf

Ah, sure, that makes sense.  I was trying to abstract it away, but I see how it's nice to see it all at once. Thanks!

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
---
 tests/modules/nf-core/ashlar/main.nf | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index 942e44deb4b..a3383df00b8 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -6,7 +6,23 @@ include { ASHLAR } from '../../../../modules/nf-core/ashlar/main.nf'
 include { ASHLAR as ASHLAR_TILE } from '../../../../modules/nf-core/ashlar/main.nf'
 
 // we zero out the UUID of output tiff images with ZERO_UUID so we get a consistent md5sum
-include { ZERO_UUID } from './zero_uuid.nf'
+process ZERO_UUID {
+
+    input:
+    val(file_in)
+    val(offset)
+
+    when:
+    file_in != "versions.yml"
+
+    script:
+    def file_path = file_in[1]
+
+    """
+    echo -n "00000000-0000-0000-0000-000000000000" | dd of=$file_path bs=1 seek=$offset conv=notrunc
+    """
+
+}
 
 workflow test_ashlar_1_file {
 

From 50d4a6cf8f84e86f687910fbbc52f94e0ccb993c Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Fri, 4 Aug 2023 11:00:58 -0400
Subject: [PATCH 106/114] broken change for discussion

---
 tests/modules/nf-core/ashlar/main.nf | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index a3383df00b8..cece758ca8d 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -9,17 +9,16 @@ include { ASHLAR as ASHLAR_TILE } from '../../../../modules/nf-core/ashlar/main.
 process ZERO_UUID {
 
     input:
-    val(file_in)
+    val(meta), path(tif)
     val(offset)
 
     when:
-    file_in != "versions.yml"
+    tif != "versions.yml"
 
     script:
-    def file_path = file_in[1]
 
     """
-    echo -n "00000000-0000-0000-0000-000000000000" | dd of=$file_path bs=1 seek=$offset conv=notrunc
+    echo -n "00000000-0000-0000-0000-000000000000" | dd of=$tif bs=1 seek=$offset conv=notrunc
     """
 
 }

From 4521bb8891b105e50f27ca002b4cf0ca06109bc9 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Fri, 4 Aug 2023 13:54:41 -0400
Subject: [PATCH 107/114] Update tests/modules/nf-core/ashlar/main.nf

Oh! sorry, I see. I missed the `tuple` before `val(meta), path(tif)` when I was testing the change.  I should have realized that!

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
---
 tests/modules/nf-core/ashlar/main.nf | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index cece758ca8d..c6d8d82ca02 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -9,9 +9,11 @@ include { ASHLAR as ASHLAR_TILE } from '../../../../modules/nf-core/ashlar/main.
 process ZERO_UUID {
 
     input:
-    val(meta), path(tif)
+    tuple val(meta), path(tif)
     val(offset)
-
+    
+    output:
+    tuple val(meta), path(tif), includeInputs: true, emit: parsed_tif
     when:
     tif != "versions.yml"
 

From 056a24098a3dda6fec5c3b869b088029a6c80896 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Fri, 4 Aug 2023 14:09:40 -0400
Subject: [PATCH 108/114] fixed zero_uuid output bug

---
 tests/modules/nf-core/ashlar/main.nf  |  6 ++----
 tests/modules/nf-core/ashlar/test.yml | 12 +++++++++++-
 2 files changed, 13 insertions(+), 5 deletions(-)

diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index c6d8d82ca02..0bd519fe7f6 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -11,11 +11,9 @@ process ZERO_UUID {
     input:
     tuple val(meta), path(tif)
     val(offset)
-    
+
     output:
-    tuple val(meta), path(tif), includeInputs: true, emit: parsed_tif
-    when:
-    tif != "versions.yml"
+    tuple val(meta), path(tif), emit: parsed_tif
 
     script:
 
diff --git a/tests/modules/nf-core/ashlar/test.yml b/tests/modules/nf-core/ashlar/test.yml
index 7e851355255..78629c71d81 100644
--- a/tests/modules/nf-core/ashlar/test.yml
+++ b/tests/modules/nf-core/ashlar/test.yml
@@ -1,11 +1,13 @@
 - name: ashlar test_ashlar_1_file
-  command: nextflow run -entry test_ashlar_1_file -plugins nf-validation tests/modules/nf-core/ashlar/main.nf -c tests/config/nextflow.config --input /home/pollen/github/modules/tests/modules/nf-core/ashlar/test_sheet_url.csv
+  command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_1_file -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
   tags:
     - ashlar
   files:
     - path: output/ashlar/ashlar_output.ome.tif
       md5sum: 796fa3687d4ff1389567c22eafb1e4cf
     - path: output/ashlar/versions.yml
+    - path: output/zero/ashlar_output.ome.tif
+      md5sum: 796fa3687d4ff1389567c22eafb1e4cf
 
 - name: ashlar test_ashlar_all_files
   command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_all_files -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
@@ -15,6 +17,8 @@
     - path: output/ashlar/ashlar_output.ome.tif
       md5sum: 576bc81fa8d678547e87d25c403ed3a4
     - path: output/ashlar/versions.yml
+    - path: output/zero/ashlar_output.ome.tif
+      md5sum: 576bc81fa8d678547e87d25c403ed3a4
 
 - name: ashlar test_ashlar_all_files_tile_size
   command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_all_files_tile_size -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
@@ -24,6 +28,8 @@
     - path: output/ashlar/ashlar_output.ome.tif
       md5sum: fb34bb112d0c95698afa76095e12085f
     - path: output/ashlar/versions.yml
+    - path: output/zero/ashlar_output.ome.tif
+      md5sum: fb34bb112d0c95698afa76095e12085f
 
 - name: ashlar test_ashlar_all_files_dfp_ffp
   command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_all_files_dfp_ffp -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
@@ -33,6 +39,8 @@
     - path: output/ashlar/ashlar_output.ome.tif
       md5sum: 576bc81fa8d678547e87d25c403ed3a4
     - path: output/ashlar/versions.yml
+    - path: output/zero/ashlar_output.ome.tif
+      md5sum: 576bc81fa8d678547e87d25c403ed3a4
 
 - name: ashlar test_ashlar_1_file_dfp_ffp
   command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_1_file_dfp_ffp -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
@@ -42,3 +50,5 @@
     - path: output/ashlar/ashlar_output.ome.tif
       md5sum: 796fa3687d4ff1389567c22eafb1e4cf
     - path: output/ashlar/versions.yml
+    - path: output/zero/ashlar_output.ome.tif
+      md5sum: 796fa3687d4ff1389567c22eafb1e4cf

From b92c0859ae79af05fb0526db5ae42a8d869f00f6 Mon Sep 17 00:00:00 2001
From: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Date: Fri, 11 Aug 2023 05:54:00 +0000
Subject: [PATCH 109/114] Use sed to remove UUID inside main module

---
 modules/nf-core/ashlar/main.nf            |  4 +++
 tests/modules/nf-core/ashlar/main.nf      | 28 ------------------
 tests/modules/nf-core/ashlar/test.yml     | 35 ++++++++++-------------
 tests/modules/nf-core/ashlar/zero_uuid.nf | 21 --------------
 4 files changed, 19 insertions(+), 69 deletions(-)
 delete mode 100644 tests/modules/nf-core/ashlar/zero_uuid.nf

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 79e4d2ce172..e88f8f1b4c9 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -21,6 +21,7 @@ process ASHLAR {
 
     script:
     def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
     def dfp = opt_dfp ? "--dfp $opt_dfp" : ""
     def ffp = opt_ffp ? "--ffp $opt_ffp" : ""
     def num_files = images instanceof List ? images.size() : 1
@@ -35,11 +36,14 @@ process ASHLAR {
     """
 
     ashlar \\
+        -o ${prefix}.ome.tif \\
         $images \\
         $args \\
         $dfp \\
         $ffp
 
+    sed -i 's/UUID="urn:uuid:[[:xdigit:]]{8}-[[:xdigit:]]{4}-[[:xdigit:]]{4}-[[:xdigit:]]{4}-[[:xdigit:]]{12}"/UUID="urn:uuid:00000000-0000-0000-0000-000000000000"/g' ${prefix}.ome.tif
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         ashlar: \$(ashlar --version 2>&1 | sed 's/^.*ashlar //; s/Using.*\$//' )
diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
index 0bd519fe7f6..278bc3195c7 100644
--- a/tests/modules/nf-core/ashlar/main.nf
+++ b/tests/modules/nf-core/ashlar/main.nf
@@ -5,24 +5,6 @@ nextflow.enable.dsl = 2
 include { ASHLAR } from '../../../../modules/nf-core/ashlar/main.nf'
 include { ASHLAR as ASHLAR_TILE } from '../../../../modules/nf-core/ashlar/main.nf'
 
-// we zero out the UUID of output tiff images with ZERO_UUID so we get a consistent md5sum
-process ZERO_UUID {
-
-    input:
-    tuple val(meta), path(tif)
-    val(offset)
-
-    output:
-    tuple val(meta), path(tif), emit: parsed_tif
-
-    script:
-
-    """
-    echo -n "00000000-0000-0000-0000-000000000000" | dd of=$tif bs=1 seek=$offset conv=notrunc
-    """
-
-}
-
 workflow test_ashlar_1_file {
 
     input_list =  [ [ id:'test_all' ],
@@ -32,8 +14,6 @@ workflow test_ashlar_1_file {
 
     ASHLAR ( input_list, [], [] )
 
-    ZERO_UUID ( ASHLAR.out.tif, "8390123" )
-
 }
 
 workflow test_ashlar_all_files {
@@ -51,8 +31,6 @@ workflow test_ashlar_all_files {
 
     ASHLAR ( input_list, [], [] )
 
-    ZERO_UUID ( ASHLAR.out.tif, "25169643" )
-
 }
 
 workflow test_ashlar_all_files_tile_size {
@@ -70,8 +48,6 @@ workflow test_ashlar_all_files_tile_size {
 
     ASHLAR_TILE ( input_list, [], [] )
 
-    ZERO_UUID ( ASHLAR_TILE.out.tif, "12586923" )
-
 }
 
 workflow test_ashlar_all_files_dfp_ffp {
@@ -94,8 +70,6 @@ workflow test_ashlar_all_files_dfp_ffp {
                                                ['ome-tiff']
                                                ['cycif_tonsil_ffp'], checkIfExists: true)] )
 
-    ZERO_UUID ( ASHLAR.out.tif, "25169643" )
-
 }
 
 workflow test_ashlar_1_file_dfp_ffp {
@@ -112,7 +86,5 @@ workflow test_ashlar_1_file_dfp_ffp {
                                                ['ome-tiff']
                                                ['cycif_tonsil_ffp'], checkIfExists: true)] )
 
-    ZERO_UUID ( ASHLAR.out.tif, "8390123" )
-
 }
 
diff --git a/tests/modules/nf-core/ashlar/test.yml b/tests/modules/nf-core/ashlar/test.yml
index 78629c71d81..92eb45f997f 100644
--- a/tests/modules/nf-core/ashlar/test.yml
+++ b/tests/modules/nf-core/ashlar/test.yml
@@ -3,52 +3,47 @@
   tags:
     - ashlar
   files:
-    - path: output/ashlar/ashlar_output.ome.tif
-      md5sum: 796fa3687d4ff1389567c22eafb1e4cf
+    - path: output/ashlar/test_all.ome.tif
+      contains:
+        - "# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead "
     - path: output/ashlar/versions.yml
-    - path: output/zero/ashlar_output.ome.tif
-      md5sum: 796fa3687d4ff1389567c22eafb1e4cf
 
 - name: ashlar test_ashlar_all_files
   command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_all_files -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
   tags:
     - ashlar
   files:
-    - path: output/ashlar/ashlar_output.ome.tif
-      md5sum: 576bc81fa8d678547e87d25c403ed3a4
+    - path: output/ashlar/test_all.ome.tif
+      contains:
+        - "# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead "
     - path: output/ashlar/versions.yml
-    - path: output/zero/ashlar_output.ome.tif
-      md5sum: 576bc81fa8d678547e87d25c403ed3a4
 
 - name: ashlar test_ashlar_all_files_tile_size
   command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_all_files_tile_size -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
   tags:
     - ashlar
   files:
-    - path: output/ashlar/ashlar_output.ome.tif
-      md5sum: fb34bb112d0c95698afa76095e12085f
+    - path: output/ashlar/test_all.ome.tif
+      contains:
+        - "# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead "
     - path: output/ashlar/versions.yml
-    - path: output/zero/ashlar_output.ome.tif
-      md5sum: fb34bb112d0c95698afa76095e12085f
 
 - name: ashlar test_ashlar_all_files_dfp_ffp
   command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_all_files_dfp_ffp -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
   tags:
     - ashlar
   files:
-    - path: output/ashlar/ashlar_output.ome.tif
-      md5sum: 576bc81fa8d678547e87d25c403ed3a4
+    - path: output/ashlar/test_all.ome.tif
+      contains:
+        - "# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead "
     - path: output/ashlar/versions.yml
-    - path: output/zero/ashlar_output.ome.tif
-      md5sum: 576bc81fa8d678547e87d25c403ed3a4
 
 - name: ashlar test_ashlar_1_file_dfp_ffp
   command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_1_file_dfp_ffp -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
   tags:
     - ashlar
   files:
-    - path: output/ashlar/ashlar_output.ome.tif
-      md5sum: 796fa3687d4ff1389567c22eafb1e4cf
+    - path: output/ashlar/test_all.ome.tif
+      contains:
+        - "# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead "
     - path: output/ashlar/versions.yml
-    - path: output/zero/ashlar_output.ome.tif
-      md5sum: 796fa3687d4ff1389567c22eafb1e4cf
diff --git a/tests/modules/nf-core/ashlar/zero_uuid.nf b/tests/modules/nf-core/ashlar/zero_uuid.nf
deleted file mode 100644
index de6ddc5a452..00000000000
--- a/tests/modules/nf-core/ashlar/zero_uuid.nf
+++ /dev/null
@@ -1,21 +0,0 @@
-nextflow.enable.dsl=2
-
-process ZERO_UUID {
-
-    input:
-    val(file_in)
-    val(offset)
-
-    when:
-    file_in != "versions.yml"
-
-    script:
-    def file_path = file_in[1]
-
-    """
-
-    echo -n "00000000-0000-0000-0000-000000000000" | dd of=$file_path bs=1 seek=$offset conv=notrunc
-
-    """
-
-}

From 440f1404937e97722af15e2da7cda4cee609cb0a Mon Sep 17 00:00:00 2001
From: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Date: Fri, 11 Aug 2023 06:53:08 +0000
Subject: [PATCH 110/114] Fixed sed

---
 modules/nf-core/ashlar/main.nf        |  5 +++--
 tests/modules/nf-core/ashlar/test.yml | 15 +++++----------
 2 files changed, 8 insertions(+), 12 deletions(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index e88f8f1b4c9..38f4ccafc72 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -36,13 +36,14 @@ process ASHLAR {
     """
 
     ashlar \\
-        -o ${prefix}.ome.tif \\
+        -o ${prefix}.uuid.ome.tif \\
         $images \\
         $args \\
         $dfp \\
         $ffp
 
-    sed -i 's/UUID="urn:uuid:[[:xdigit:]]{8}-[[:xdigit:]]{4}-[[:xdigit:]]{4}-[[:xdigit:]]{4}-[[:xdigit:]]{12}"/UUID="urn:uuid:00000000-0000-0000-0000-000000000000"/g' ${prefix}.ome.tif
+    sed -E 's/UUID="urn:uuid:[[:xdigit:]]{8}-[[:xdigit:]]{4}-[[:xdigit:]]{4}-[[:xdigit:]]{4}-[[:xdigit:]]{12}"/UUID="urn:uuid:00000000-0000-0000-0000-000000000000"/g' ${prefix}.uuid.ome.tif > ${prefix}.ome.tif
+    rm ${prefix}.uuid.ome.tif
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/tests/modules/nf-core/ashlar/test.yml b/tests/modules/nf-core/ashlar/test.yml
index 92eb45f997f..e2e717cc9c8 100644
--- a/tests/modules/nf-core/ashlar/test.yml
+++ b/tests/modules/nf-core/ashlar/test.yml
@@ -4,8 +4,7 @@
     - ashlar
   files:
     - path: output/ashlar/test_all.ome.tif
-      contains:
-        - "# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead "
+      md5sum: 796fa3687d4ff1389567c22eafb1e4cf
     - path: output/ashlar/versions.yml
 
 - name: ashlar test_ashlar_all_files
@@ -14,8 +13,7 @@
     - ashlar
   files:
     - path: output/ashlar/test_all.ome.tif
-      contains:
-        - "# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead "
+      md5sum: 576bc81fa8d678547e87d25c403ed3a4
     - path: output/ashlar/versions.yml
 
 - name: ashlar test_ashlar_all_files_tile_size
@@ -24,8 +22,7 @@
     - ashlar
   files:
     - path: output/ashlar/test_all.ome.tif
-      contains:
-        - "# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead "
+      md5sum: fb34bb112d0c95698afa76095e12085f
     - path: output/ashlar/versions.yml
 
 - name: ashlar test_ashlar_all_files_dfp_ffp
@@ -34,8 +31,7 @@
     - ashlar
   files:
     - path: output/ashlar/test_all.ome.tif
-      contains:
-        - "# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead "
+      md5sum: 576bc81fa8d678547e87d25c403ed3a4
     - path: output/ashlar/versions.yml
 
 - name: ashlar test_ashlar_1_file_dfp_ffp
@@ -44,6 +40,5 @@
     - ashlar
   files:
     - path: output/ashlar/test_all.ome.tif
-      contains:
-        - "# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead "
+      md5sum: 796fa3687d4ff1389567c22eafb1e4cf
     - path: output/ashlar/versions.yml

From 10bf81eb99907eca859a6f634d5c5ad428335009 Mon Sep 17 00:00:00 2001
From: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Date: Fri, 11 Aug 2023 14:35:32 +0100
Subject: [PATCH 111/114] Update modules/nf-core/ashlar/main.nf

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
---
 modules/nf-core/ashlar/main.nf | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 38f4ccafc72..b581ee7b4f3 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -20,13 +20,13 @@ process ASHLAR {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    def dfp = opt_dfp ? "--dfp $opt_dfp" : ""
-    def ffp = opt_ffp ? "--ffp $opt_ffp" : ""
-    def num_files = images instanceof List ? images.size() : 1
-    def opt_dfp_size = opt_dfp instanceof List ? opt_dfp.size() : 1
-    def opt_ffp_size = opt_ffp instanceof List ? opt_ffp.size() : 1
+    def args          = task.ext.args           ?: ''
+    def prefix        = task.ext.prefix         ?: "${meta.id}"
+    def dfp           = opt_dfp                 ? "--dfp $opt_dfp" : ""
+    def ffp           = opt_ffp                 ? "--ffp $opt_ffp" : ""
+    def num_files     = images instanceof List  ? images.size()    : 1
+    def opt_dfp_size  = opt_dfp instanceof List ? opt_dfp.size()   : 1
+    def opt_ffp_size  = opt_ffp instanceof List ? opt_ffp.size()   : 1
     def dfp_validated = (opt_dfp_size == 0 || opt_dfp_size == 1 || opt_dfp_size == num_files) ? true : false
     def ffp_validated = (opt_ffp_size == 0 || opt_ffp_size == 1 || opt_ffp_size == num_files) ? true : false
 

From 7fa6f95da01748108ce6dadf3ba6aaf3f514a76f Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Fri, 11 Aug 2023 11:51:40 -0400
Subject: [PATCH 112/114] proposed change to sed command

---
 modules/nf-core/ashlar/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index b581ee7b4f3..85ec88ed704 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -42,7 +42,7 @@ process ASHLAR {
         $dfp \\
         $ffp
 
-    sed -E 's/UUID="urn:uuid:[[:xdigit:]]{8}-[[:xdigit:]]{4}-[[:xdigit:]]{4}-[[:xdigit:]]{4}-[[:xdigit:]]{12}"/UUID="urn:uuid:00000000-0000-0000-0000-000000000000"/g' ${prefix}.uuid.ome.tif > ${prefix}.ome.tif
+    sed -E 's/UUID="urn:uuid:[[:xdigit:]]{8}-[[:xdigit:]]{4}-[[:xdigit:]]{4}-[[:xdigit:]]{4}-[[:xdigit:]]{12}"/                                                    /g' ${prefix}.uuid.ome.tif > ${prefix}.ome.tif
     rm ${prefix}.uuid.ome.tif
 
     cat <<-END_VERSIONS > versions.yml

From 7988e552b9df2380d6aff6196b5b687a5132df8f Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Fri, 11 Aug 2023 13:57:28 -0400
Subject: [PATCH 113/114] adding modified test.yml file

---
 tests/modules/nf-core/ashlar/test.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tests/modules/nf-core/ashlar/test.yml b/tests/modules/nf-core/ashlar/test.yml
index e2e717cc9c8..be9450cc22d 100644
--- a/tests/modules/nf-core/ashlar/test.yml
+++ b/tests/modules/nf-core/ashlar/test.yml
@@ -4,7 +4,7 @@
     - ashlar
   files:
     - path: output/ashlar/test_all.ome.tif
-      md5sum: 796fa3687d4ff1389567c22eafb1e4cf
+      md5sum: ae98ac74e3c818bb26c99ba4b9c2dd51
     - path: output/ashlar/versions.yml
 
 - name: ashlar test_ashlar_all_files
@@ -13,7 +13,7 @@
     - ashlar
   files:
     - path: output/ashlar/test_all.ome.tif
-      md5sum: 576bc81fa8d678547e87d25c403ed3a4
+      md5sum: 5f4165203545b7efe04ed5f4a6d5ac9d
     - path: output/ashlar/versions.yml
 
 - name: ashlar test_ashlar_all_files_tile_size
@@ -22,7 +22,7 @@
     - ashlar
   files:
     - path: output/ashlar/test_all.ome.tif
-      md5sum: fb34bb112d0c95698afa76095e12085f
+      md5sum: acee3aeaf7ea088062b2c15eff72dfb4
     - path: output/ashlar/versions.yml
 
 - name: ashlar test_ashlar_all_files_dfp_ffp
@@ -31,7 +31,7 @@
     - ashlar
   files:
     - path: output/ashlar/test_all.ome.tif
-      md5sum: 576bc81fa8d678547e87d25c403ed3a4
+      md5sum: 5f4165203545b7efe04ed5f4a6d5ac9d
     - path: output/ashlar/versions.yml
 
 - name: ashlar test_ashlar_1_file_dfp_ffp
@@ -40,5 +40,5 @@
     - ashlar
   files:
     - path: output/ashlar/test_all.ome.tif
-      md5sum: 796fa3687d4ff1389567c22eafb1e4cf
+      md5sum: ae98ac74e3c818bb26c99ba4b9c2dd51
     - path: output/ashlar/versions.yml

From 4aa7498eb1b14ca4c821cfcda8948d358cf10275 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Mon, 14 Aug 2023 11:25:20 -0400
Subject: [PATCH 114/114] reverted to in-place sed

---
 modules/nf-core/ashlar/main.nf | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 85ec88ed704..2316b024391 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -36,14 +36,13 @@ process ASHLAR {
     """
 
     ashlar \\
-        -o ${prefix}.uuid.ome.tif \\
+        -o ${prefix}.ome.tif \\
         $images \\
         $args \\
         $dfp \\
         $ffp
 
-    sed -E 's/UUID="urn:uuid:[[:xdigit:]]{8}-[[:xdigit:]]{4}-[[:xdigit:]]{4}-[[:xdigit:]]{4}-[[:xdigit:]]{12}"/                                                    /g' ${prefix}.uuid.ome.tif > ${prefix}.ome.tif
-    rm ${prefix}.uuid.ome.tif
+    sed -i -E 's/UUID="urn:uuid:[[:xdigit:]]{8}-[[:xdigit:]]{4}-[[:xdigit:]]{4}-[[:xdigit:]]{4}-[[:xdigit:]]{12}"/                                                    /g' ${prefix}.ome.tif
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":