Fix centrifuge: reduce number of input channels (nf-core#3674)

* Bump taxpasta version (biocontainer not yet available) * Remove unnecessary (and sometimes problematic) input channel * Improve output glob for optional alignments * Remove now unnecessary variable from command * linting * Add missing args
limrp · Jul 28, 2023 · 0f30afb · 0f30afb
1 parent c381236
commit 0f30afb
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Showing 3 changed files with 10 additions and 10 deletions.
diff --git a/modules/nf-core/centrifuge/centrifuge/main.nf b/modules/nf-core/centrifuge/centrifuge/main.nf
@@ -12,12 +12,11 @@ process CENTRIFUGE_CENTRIFUGE {
     path db
     val save_unaligned
     val save_aligned
-    val sam_format
 
     output:
     tuple val(meta), path('*report.txt')                 , emit: report
     tuple val(meta), path('*results.txt')                , emit: results
-    tuple val(meta), path('*.sam')                       , optional: true, emit: sam
+    tuple val(meta), path('*.{sam,tab}')                 , optional: true, emit: sam
     tuple val(meta), path('*.mapped.fastq{,.1,.2}.gz')   , optional: true, emit: fastq_mapped
     tuple val(meta), path('*.unmapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_unmapped
     path "versions.yml"                                  , emit: versions
@@ -38,7 +37,6 @@ process CENTRIFUGE_CENTRIFUGE {
         unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
         aligned = save_aligned ? "--al-conc-gz ${prefix}.mapped.fastq.gz" : ''
     }
-    def sam_output = sam_format ? "--out-fmt 'sam'" : ''
     """
     ## we add "-no-name ._" to ensure silly Mac OSX metafiles files aren't included
     db_name=`find -L ${db} -name "*.1.cf" -not -name "._*"  | sed 's/\\.1.cf\$//'`
@@ -50,7 +48,6 @@ process CENTRIFUGE_CENTRIFUGE {
         -S ${prefix}.results.txt \\
         $unaligned \\
         $aligned \\
-        $sam_output \\
         $args
 
     cat <<-END_VERSIONS > versions.yml

diff --git a/modules/nf-core/centrifuge/centrifuge/meta.yml b/modules/nf-core/centrifuge/centrifuge/meta.yml
@@ -27,10 +27,10 @@ input:
       type: directory
       description: Path to directory containing centrifuge database files
   - save_unaligned:
-      type: value
+      type: boolean
       description: If true unmapped fastq files are saved
   - save_aligned:
-      type: value
+      type: boolean
       description: If true mapped fastq files are saved
 output:
   - meta:
@@ -48,6 +48,11 @@ output:
       description: |
         File containing classification results
       pattern: "*.{results.txt}"
+  - sam:
+      type: file
+      description: |
+        Optional output file containing read alignments (SAM format )or a table of per-read hit information (TAB)s
+      pattern: "*.{sam,tab}"
   - fastq_unmapped:
       type: file
       description: Unmapped fastq files

diff --git a/tests/modules/nf-core/centrifuge/centrifuge/main.nf b/tests/modules/nf-core/centrifuge/centrifuge/main.nf
@@ -12,10 +12,9 @@ workflow test_centrifuge_centrifuge_single_end {
     db    =  [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/minigut_cf.tar.gz', checkIfExists: true) ]
     save_unaligned = true
     save_aligned = false
-    sam_format = false
 
     UNTAR ( db )
-    CENTRIFUGE_CENTRIFUGE ( input, UNTAR.out.untar.map{ it[1] }, save_unaligned, save_aligned, sam_format )
+    CENTRIFUGE_CENTRIFUGE ( input, UNTAR.out.untar.map{ it[1] }, save_unaligned, save_aligned )
 
 }
 
@@ -27,10 +26,9 @@ workflow test_centrifuge_centrifuge_paired_end {
      db    =  [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/minigut_cf.tar.gz', checkIfExists: true) ]
      save_unaligned = true
      save_aligned = false
-     sam_format = false
 
     UNTAR ( db )
-    CENTRIFUGE_CENTRIFUGE ( input, UNTAR.out.untar.map{ it[1] }, save_unaligned, save_aligned, sam_format )
+    CENTRIFUGE_CENTRIFUGE ( input, UNTAR.out.untar.map{ it[1] }, save_unaligned, save_aligned )
 
 
 }