Move conda-checks (fifth batch) (nf-core#3704)

* Moving conda-check and replacing exit 1 with error-cmd

* Adding keywords to meta-file for katgc

* Adding keywords to meta-file for merquryfk

* test-data was seemingly moved to new subdir

* Fixing outdir of unzipped test-data

* Disabling conda-based test of hlala/preparegraph as that module does not support conda

.github/workflows/test.yml

@@ -184,6 +184,8 @@ jobs:
             tags: gatk4/postprocessgermlinecnvcalls
           - profile: "conda"
             tags: genescopefk
+          - profile: "conda"
+            tags: hlala/preparegraph
           - profile: "conda"
             tags: ilastik/multicut
           - profile: "conda"

modules/nf-core/genescopefk/main.nf

@@ -5,11 +5,6 @@ process GENESCOPEFK {
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     container 'ghcr.io/nbisweden/fastk_genescopefk_merquryfk:1.2'
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "GENESCOPEFK module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     tuple val(meta), path(fastk_histex_histogram)
 
@@ -26,6 +21,11 @@ process GENESCOPEFK {
     task.ext.when == null || task.ext.when
 
     script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "GENESCOPEFK module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def GENESCOPE_VERSION = '380815c420f50171f9234a0fd1ff426b39829b91' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.

modules/nf-core/hlala/preparegraph/main.nf

@@ -2,21 +2,13 @@ process HLALA_PREPAREGRAPH {
     tag "$meta.id"
     label 'process_high'
 
-
-
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hla-la:1.0.3--hd03093a_0':
         'biocontainers/hla-la:1.0.3--hd03093a_0' }"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "HLALA_PREPAREGRAPH module does not support Conda. Please use Docker or Singularity."
-    }
-
     input:
     tuple val(meta), path(graph)
 
-
     output:
     tuple val(meta), path("${graph}")        , emit: graph
     path "versions.yml", emit: versions
@@ -25,6 +17,10 @@ process HLALA_PREPAREGRAPH {
     task.ext.when == null || task.ext.when
 
     script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "HLALA_PREPAREGRAPH module does not support Conda. Please use Docker or Singularity."
+    }
     def args = task.ext.args ?: ''
 
     """

modules/nf-core/ilastik/multicut/main.nf

@@ -2,11 +2,6 @@ process ILASTIK_MULTICUT {
     tag "$meta.id"
     label 'process_low'
 
-
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "ILASTIK_MULTICUT module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
     container "docker.io/biocontainers/ilastik:1.4.0_cv1"
 
     input:
@@ -22,6 +17,10 @@ process ILASTIK_MULTICUT {
     task.ext.when == null || task.ext.when
 
     script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "ILASTIK_MULTICUT module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
@@ -43,6 +42,10 @@ process ILASTIK_MULTICUT {
     """
 
     stub:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "ILASTIK_MULTICUT module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def prefix = task.ext.prefix ?: "${meta.id}"
     def VERSION = "1.4.0" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """

modules/nf-core/ilastik/pixelclassification/main.nf

@@ -2,10 +2,6 @@ process ILASTIK_PIXELCLASSIFICATION {
     tag "$meta.id"
     label 'process_single'
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "ILASTIK_PIXELCLASSIFICATION module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
     container "docker.io/biocontainers/ilastik:1.4.0_cv1"
 
     input:
@@ -20,6 +16,10 @@ process ILASTIK_PIXELCLASSIFICATION {
     task.ext.when == null || task.ext.when
 
     script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "ILASTIK_PIXELCLASSIFICATION module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     suffix = task.ext.suffix ?: "h5"
@@ -40,6 +40,10 @@ process ILASTIK_PIXELCLASSIFICATION {
     """
 
     stub:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "ILASTIK_PIXELCLASSIFICATION module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def prefix = task.ext.prefix ?: "${meta.id}"
     suffix = task.ext.suffix ?: "h5"
 

modules/nf-core/merquryfk/katcomp/main.nf

@@ -5,11 +5,6 @@ process MERQURYFK_KATCOMP {
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     container 'ghcr.io/nbisweden/fastk_genescopefk_merquryfk:1.2'
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "MERQURYFK_KATCOMP module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     tuple val(meta), path(fastk1_hist), path(fastk1_ktab), path(fastk2_hist), path(fastk2_ktab)
 
@@ -26,6 +21,10 @@ process MERQURYFK_KATCOMP {
     task.ext.when == null || task.ext.when
 
     script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "MERQURYFK_KATCOMP module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def FASTK_VERSION = 'f18a4e6d2207539f7b84461daebc54530a9559b0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.

modules/nf-core/merquryfk/katgc/main.nf

@@ -5,11 +5,6 @@ process MERQURYFK_KATGC {
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     container 'ghcr.io/nbisweden/fastk_genescopefk_merquryfk:1.2'
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "MERQURYFK_KATGC module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     tuple val(meta), path(fastk_hist), path(fastk_ktab)
 
@@ -26,6 +21,10 @@ process MERQURYFK_KATGC {
     task.ext.when == null || task.ext.when
 
     script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "MERQURYFK_KATGC module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def FASTK_VERSION   = 'f18a4e6d2207539f7b84461daebc54530a9559b0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.

modules/nf-core/merquryfk/katgc/meta.yml

@@ -1,8 +1,10 @@
 name: "merquryfk_katgc"
-description: A reimplemenation of Kat GC to work with FastK databases
+description: A reimplemenation of KatGC to work with FastK databases
 keywords:
-  - k-mer
+  - k-mer frequency
   - GC content
+  - 3D heat map
+  - contour map
 tools:
   - "merquryfk":
       description: "FastK based version of Merqury"

modules/nf-core/merquryfk/merquryfk/main.nf

@@ -5,11 +5,6 @@ process MERQURYFK_MERQURYFK {
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     container 'ghcr.io/nbisweden/fastk_genescopefk_merquryfk:1.2'
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "MERQURYFK_MERQURYFK module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     tuple val(meta), path(fastk_hist), path(fastk_ktab), path(assembly), path(haplotigs)
 
@@ -36,6 +31,10 @@ process MERQURYFK_MERQURYFK {
     task.ext.when == null || task.ext.when
 
     script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "MERQURYFK_MERQURYFK module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
     def FASTK_VERSION = 'f18a4e6d2207539f7b84461daebc54530a9559b0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.

modules/nf-core/merquryfk/merquryfk/meta.yml

@@ -1,7 +1,9 @@
 name: "merquryfk_merquryfk"
 description: FastK based version of Merqury
 keywords:
-  - sort
+  - Merqury
+  - reference-free
+  - assembly evaluation
 tools:
   - "merquryfk":
       description: "FastK based version of Merqury"

tests/modules/nf-core/hlala/preparegraph/main.nf

@@ -14,7 +14,7 @@ workflow test_hlala_preparegraph {
     UNZIP( input )
 
     UNZIP.out.unzipped_archive.map { id, path ->
-                                        [ id, "$path/${path.toString().split("/").last()}" ] 
+                                        [ id, "$path/PRG_${path.toString().split("/").last()}" ] 
                                      }
                                      .set { hla_preparegraph_test_in }
 

tests/modules/nf-core/hlala/preparegraph/test.yml

@@ -54,53 +54,53 @@
     - path: output/hlala/PRG_test/translation/100.txt
       md5sum: 8dd91725d9a2f1f71a82ae1d190aa840
     - path: output/hlala/versions.yml
-    - path: output/unzip/PRG_test/PRG_test/.nextflow.log
+    - path: output/unzip/test/PRG_test/.nextflow.log
       md5sum: f22b6ca679424bea221fe100b4162b4a
-    - path: output/unzip/PRG_test/PRG_test/PRG/100_gene_HLA-A_9_exon_5.txt
+    - path: output/unzip/test/PRG_test/PRG/100_gene_HLA-A_9_exon_5.txt
       md5sum: fa4f97441bdd999f3ada1a49e67b726b
-    - path: output/unzip/PRG_test/PRG_test/PRG/100_gene_HLA-A_9_exon_5.txt.graph
+    - path: output/unzip/test/PRG_test/PRG/100_gene_HLA-A_9_exon_5.txt.graph
       md5sum: 0c5532614ffa94e30321c521e5a5046e
-    - path: output/unzip/PRG_test/PRG_test/PRG/graph.txt
+    - path: output/unzip/test/PRG_test/PRG/graph.txt
       md5sum: 434932977b863df94d3ada073b7636cf
-    - path: output/unzip/PRG_test/PRG_test/PRG/positions.txt
+    - path: output/unzip/test/PRG_test/PRG/positions.txt
       md5sum: 9f97b556f9ddf0414ffeaeb568bfb81f
-    - path: output/unzip/PRG_test/PRG_test/PRG/segments.txt
+    - path: output/unzip/test/PRG_test/PRG/segments.txt
       md5sum: b60e45e75e63e5fde13bb9bea4a4a079
-    - path: output/unzip/PRG_test/PRG_test/extendedReferenceGenome/extendedReferenceGenome.fa
+    - path: output/unzip/test/PRG_test/extendedReferenceGenome/extendedReferenceGenome.fa
       md5sum: c2e7c88c3ec5bfe966fb9204689dffc9
-    - path: output/unzip/PRG_test/PRG_test/knownReferences/1000G_B37_noChr.txt
+    - path: output/unzip/test/PRG_test/knownReferences/1000G_B37_noChr.txt
       md5sum: df42b5bbf6a2de7c8a4fa0a04176b614
-    - path: output/unzip/PRG_test/PRG_test/knownReferences/1000G_B38.txt
+    - path: output/unzip/test/PRG_test/knownReferences/1000G_B38.txt
       md5sum: 252cc753ecdaf8e76102511d2ec7ff57
-    - path: output/unzip/PRG_test/PRG_test/knownReferences/B37_generic_noChr.txt
+    - path: output/unzip/test/PRG_test/knownReferences/B37_generic_noChr.txt
       md5sum: 35652c6d147a3182d1e4dc11c88dc5af
-    - path: output/unzip/PRG_test/PRG_test/knownReferences/PRG_MHC_GRCh38_withIMGT.txt
+    - path: output/unzip/test/PRG_test/knownReferences/PRG_MHC_GRCh38_withIMGT.txt
       md5sum: c7750bb669e8d59409bc42202da3df75
-    - path: output/unzip/PRG_test/PRG_test/mapping/100.fa
+    - path: output/unzip/test/PRG_test/mapping/100.fa
       md5sum: ecbd3efeb988c3cf2d4e6d3ff2cd92c8
-    - path: output/unzip/PRG_test/PRG_test/mapping_PRGonly/check_refSequence_length.pl
+    - path: output/unzip/test/PRG_test/mapping_PRGonly/check_refSequence_length.pl
       md5sum: ab1646b5838214ac4b1f902937a70967
-    - path: output/unzip/PRG_test/PRG_test/mapping_PRGonly/referenceGenome.fa
+    - path: output/unzip/test/PRG_test/mapping_PRGonly/referenceGenome.fa
       md5sum: 512b39c490d74bb91ce5ad1d8616e09e
-    - path: output/unzip/PRG_test/PRG_test/mapping_PRGonly/referenceGenome.fa.amb
+    - path: output/unzip/test/PRG_test/mapping_PRGonly/referenceGenome.fa.amb
       md5sum: 7b847d4f48865b52f04cce82328199c1
-    - path: output/unzip/PRG_test/PRG_test/mapping_PRGonly/referenceGenome.fa.ann
+    - path: output/unzip/test/PRG_test/mapping_PRGonly/referenceGenome.fa.ann
       md5sum: c1943aa321630550d12a435e4350dfdc
-    - path: output/unzip/PRG_test/PRG_test/mapping_PRGonly/referenceGenome.fa.bwt
-    - path: output/unzip/PRG_test/PRG_test/mapping_PRGonly/referenceGenome.fa.pac
-    - path: output/unzip/PRG_test/PRG_test/mapping_PRGonly/referenceGenome.fa.sa
-    - path: output/unzip/PRG_test/PRG_test/mapping_PRGonly/referenceGenome.fa_bowtie2idx.1.bt2
-    - path: output/unzip/PRG_test/PRG_test/mapping_PRGonly/referenceGenome.fa_bowtie2idx.2.bt2
-    - path: output/unzip/PRG_test/PRG_test/mapping_PRGonly/referenceGenome.fa_bowtie2idx.3.bt2
-    - path: output/unzip/PRG_test/PRG_test/mapping_PRGonly/referenceGenome.fa_bowtie2idx.4.bt2
-    - path: output/unzip/PRG_test/PRG_test/mapping_PRGonly/referenceGenome.fa_bowtie2idx.rev.1.bt2
-    - path: output/unzip/PRG_test/PRG_test/mapping_PRGonly/referenceGenome.fa_bowtie2idx.rev.2.bt2
-    - path: output/unzip/PRG_test/PRG_test/sequences.txt
+    - path: output/unzip/test/PRG_test/mapping_PRGonly/referenceGenome.fa.bwt
+    - path: output/unzip/test/PRG_test/mapping_PRGonly/referenceGenome.fa.pac
+    - path: output/unzip/test/PRG_test/mapping_PRGonly/referenceGenome.fa.sa
+    - path: output/unzip/test/PRG_test/mapping_PRGonly/referenceGenome.fa_bowtie2idx.1.bt2
+    - path: output/unzip/test/PRG_test/mapping_PRGonly/referenceGenome.fa_bowtie2idx.2.bt2
+    - path: output/unzip/test/PRG_test/mapping_PRGonly/referenceGenome.fa_bowtie2idx.3.bt2
+    - path: output/unzip/test/PRG_test/mapping_PRGonly/referenceGenome.fa_bowtie2idx.4.bt2
+    - path: output/unzip/test/PRG_test/mapping_PRGonly/referenceGenome.fa_bowtie2idx.rev.1.bt2
+    - path: output/unzip/test/PRG_test/mapping_PRGonly/referenceGenome.fa_bowtie2idx.rev.2.bt2
+    - path: output/unzip/test/PRG_test/sequences.txt
       md5sum: 61a3df2ca23dbe8d35c65944784def76
-    - path: output/unzip/PRG_test/PRG_test/serializedGRAPH
+    - path: output/unzip/test/PRG_test/serializedGRAPH
       md5sum: a88016a601377a967feb04c1bbeeba65
-    - path: output/unzip/PRG_test/PRG_test/serializedGRAPH_preGapPathIndex
+    - path: output/unzip/test/PRG_test/serializedGRAPH_preGapPathIndex
       md5sum: 65ea9cd52a00ffd51a2460c6887b277e
-    - path: output/unzip/PRG_test/PRG_test/translation/100.txt
+    - path: output/unzip/test/PRG_test/translation/100.txt
       md5sum: 8dd91725d9a2f1f71a82ae1d190aa840
     - path: output/unzip/versions.yml