Update trimgalore

modules/nf-core/trimgalore/environment.yml

@@ -4,6 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::cutadapt=4.9
   - bioconda::trim-galore=0.6.10
-  - conda-forge::pigz=2.8

modules/nf-core/trimgalore/main.nf

@@ -3,20 +3,20 @@ process TRIMGALORE {
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
-        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9b/9becad054093ad4083a961d12733f2a742e11728fe9aa815d678b882b3ede520/data'
-        : 'community.wave.seqera.io/library/cutadapt_trim-galore_pigz:a98edd405b34582d'}"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/trim-galore:0.6.10--hdfd78af_2' :
+        'biocontainers/trim-galore:0.6.10--hdfd78af_2'}"
 
     input:
     tuple val(meta), path(reads)
 
     output:
     tuple val(meta), path("*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz"), emit: reads
-    tuple val(meta), path("*report.txt")                               , emit: log, optional: true
-    tuple val(meta), path("*unpaired{,_1,_2}.fq.gz")                  , emit: unpaired, optional: true
-    tuple val(meta), path("*.html")                                    , emit: html, optional: true
-    tuple val(meta), path("*.zip")                                     , emit: zip, optional: true
-    path "versions.yml"					                               , emit: versions
+    tuple val(meta), path("*report.txt")                               , emit: log     , optional: true
+    tuple val(meta), path("*unpaired{,_1,_2}.fq.gz")                   , emit: unpaired, optional: true
+    tuple val(meta), path("*.html")                                    , emit: html    , optional: true
+    tuple val(meta), path("*.zip")                                     , emit: zip     , optional: true
+    tuple val("${task.process}"), val("trimgalore"), eval('trim_galore --version | grep -Eo "[0-9]+(\\.[0-9]+)+"'), topic: versions, emit: versions_trimgalore
 
     when:
     task.ext.when == null || task.ext.when
@@ -52,13 +52,6 @@ process TRIMGALORE {
             --cores ${cores} \\
             --gzip \\
             ${prefix}.fastq.gz
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')
-            cutadapt: \$(cutadapt --version)
-            pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
-        END_VERSIONS
         """
     }
     else {
@@ -72,13 +65,6 @@ process TRIMGALORE {
             --gzip \\
             ${prefix}_1.fastq.gz \\
             ${prefix}_2.fastq.gz
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')
-            cutadapt: \$(cutadapt --version)
-            pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
-        END_VERSIONS
         """
     }
 
@@ -96,12 +82,5 @@ process TRIMGALORE {
     }
     """
     ${output_command}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')
-        cutadapt: \$(cutadapt --version)
-        pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
-    END_VERSIONS
     """
 }

modules/nf-core/trimgalore/meta.yml

@@ -1,9 +1,11 @@
 name: trimgalore
-description: Trim FastQ files using Trim Galore!
+description: |
+  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files,
+  with extra functionality for RRBS data
 keywords:
   - trimming
   - adapters
-  - sequencing adapters
+  - sequencing
   - fastq
 tools:
   - trimgalore:
@@ -14,7 +16,8 @@ tools:
       homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
       documentation: https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md
       licence: ["GPL-3.0-or-later"]
-      identifier: ""
+      identifier: biotools:trim_galore
+
 input:
   - - meta:
         type: map
@@ -26,7 +29,8 @@ input:
         description: |
           List of input FastQ files of size 1 and 2 for single-end and paired-end data,
           respectively.
-        ontologies: []
+        ontologies:
+          - edam: "http://edamontology.org/format_1930" # FASTQ
 output:
   reads:
     - - meta:
@@ -35,66 +39,85 @@ output:
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
       - "*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz":
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
+          type: file
+          description: The trimmed/modified fastq reads
           pattern: "*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz"
+          ontologies:
+            - edam: "http://edamontology.org/format_1930" # FASTQ
+            - edam: http://edamontology.org/format_3989 # GZIP format
   log:
     - - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
       - "*report.txt":
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-          pattern: "*_{report.txt}"
+          type: file
+          description: trimgalore log file
+          pattern: "*report.txt"
+          ontologies:
+            - edam: "http://edamontology.org/format_2330" # Textual format
   unpaired:
     - - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
       - "*unpaired{,_1,_2}.fq.gz":
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
+          type: file
+          description: unpaired reads when --retain_unpaired flag is used
           pattern: "*unpaired*.fq.gz"
+          ontologies:
+            - edam: "http://edamontology.org/format_1930" # FASTQ
+            - edam: http://edamontology.org/format_3989 # GZIP format
   html:
     - - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
       - "*.html":
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-          pattern: "*_{fastqc.html}"
+          type: file
+          description: FastQC HTML report after trimming when the --fastqc flag is used
+          pattern: "*_fastqc.html"
+          ontologies:
+            - edam: "http://edamontology.org/format_2331" # HTML
   zip:
     - - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
       - "*.zip":
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-          pattern: "*_{fastqc.zip}"
+          type: file
+          description: FastQC report output zip after trimming when the --fastqc flag
+            is used
+          pattern: "*_fastqc.zip"
+          ontologies:
+            - edam: http://edamontology.org/format_3987 # ZIP format
+  versions_trimgalore:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - trimgalore:
+          type: string
+          description: The name of the tool
+      - trim_galore --version | grep -Eo "[0-9]+(\.[0-9]+)+":
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - trimgalore:
+          type: string
+          description: The name of the tool
+      - trim_galore --version | grep -Eo "[0-9]+(\.[0-9]+)+":
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@drpatelh"
   - "@ewels"
@@ -103,3 +126,4 @@ maintainers:
   - "@drpatelh"
   - "@ewels"
   - "@FelixKrueger"
+  - "@vagkaratzas"