trim_galore version

modules/nf-core/elprep/filter/meta.yml

@@ -115,6 +115,7 @@ output:
           type: file
           description: BAM/SAM file
           pattern: "*.{bam,sam}"
+          ontologies: []
   logs:
     - - meta:
           type: map
@@ -125,6 +126,7 @@ output:
           type: file
           description: Log file
           pattern: "elprep-*.log"
+          ontologies: []
   metrics:
     - - meta:
           type: map
@@ -135,6 +137,7 @@ output:
           type: file
           description: Metrics file
           pattern: "*.{metrics.txt}"
+          ontologies: []
   recall:
     - - meta:
           type: map
@@ -145,6 +148,7 @@ output:
           type: file
           description: Recall file
           pattern: "*.{recall}"
+          ontologies: []
   gvcf:
     - - meta:
           type: map
@@ -155,6 +159,7 @@ output:
           type: file
           description: VCF file
           pattern: "*.{vcf.gz}"
+          ontologies: []
   table:
     - - meta:
           type: map
@@ -165,6 +170,7 @@ output:
           type: file
           description: Table
           pattern: "*.{table}"
+          ontologies: []
   activity_profile:
     - - meta:
           type: map
@@ -175,6 +181,7 @@ output:
           type: file
           description: Activity profile
           pattern: "*.{activity_profile.igv}"
+          ontologies: []
   assembly_regions:
     - - meta:
           type: map
@@ -185,6 +192,7 @@ output:
           type: file
           description: Assembly regions
           pattern: "*.{assembly_regions.igv}"
+          ontologies: []
   versions:
     - versions.yml:
         type: file

modules/nf-core/trimgalore/main.nf

@@ -16,7 +16,9 @@ process TRIMGALORE {
     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("${task.process}"), val('trim_galore'), eval("trim_galore --version 2>&1 | grep -Eo '[0-9]+(\\.[0-9]+)+'"), topic: versions, emit: versions_trim_galore
+    tuple val("${task.process}"), val('cutadapt'), eval("echo \$(cutadapt --version 2>&1)"), topic: versions, emit: versions_cutadapt
+    tuple val("${task.process}"), val('pigz'), eval("echo \$( pigz --version 2>&1 | sed 's/pigz //g' )"), topic: versions, emit: versions_pigz
 
     when:
     task.ext.when == null || task.ext.when
@@ -52,13 +54,6 @@ 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 +67,6 @@ 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 +84,5 @@ 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

@@ -16,85 +16,46 @@ tools:
       licence: ["GPL-3.0-or-later"]
       identifier: ""
 input:
-  - - meta:
-        type: map
-        description: |
-          Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
-    - reads:
-        type: file
-        description: |
-          List of input FastQ files of size 1 and 2 for single-end and paired-end data,
-          respectively.
-        ontologies: []
+  - reads:
+      type: array
+      description: List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
+      ontologies: []
 output:
   reads:
-    - - meta:
-          type: map
-          description: |
-            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 ]
-          pattern: "*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz"
+    type: array # Matches the tuple val(meta), path(...) in main.nf
+    description: Trimmed FastQ file(s).
+    pattern: "*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz"
   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: Log file generated by Trim Galore!.
+    pattern: "*report.txt"
   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 ]
-          pattern: "*unpaired*.fq.gz"
+    type: file
+    description: Unpaired FastQ file(s) generated when processing paired-end data.
+    pattern: "*unpaired*.fq.gz"
   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 report HTML file generated by Trim Galore!.
+    pattern: "*.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}"
-  versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    type: array
+    # Explicitly declare that the items in the array are Files
+    items:
+      type: File 
+      description: FastQC report ZIP file generated by Trim Galore!.
+      pattern: "*.zip"
+  versions_trim_galore:
+    type: array # Matches the tuple [task.process, 'trim_galore', version]
+    description: Trim Galore! version information.
+    pattern: "*"
+  versions_cutadapt:
+    type: array
+    description: Cutadapt version information (Trim Galore! dependency).
+    pattern: "*"
+  versions_pigz:
+    type: array
+    description: pigz version information (used for parallel compression/decompression).
+    pattern: "*"
 authors:
   - "@drpatelh"
   - "@ewels"

modules/nf-core/trimgalore/tests/main.nf.test

@@ -39,7 +39,7 @@ nextflow_process {
                     { assert path(process.out.log.get(0).get(1)).getText().contains(report1_line) }
                     }
                 },
-                { assert snapshot(path(process.out.versions.get(0)).yaml).match() },
+                { assert snapshot(process.out.versions_trim_galore).match() },
             )
         }
     }
@@ -62,8 +62,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out,
-                    path(process.out.versions.get(0)).yaml
+                    process.out
                 ).match() },
             )
         }
@@ -121,7 +120,7 @@ nextflow_process {
                     { assert path(process.out.log.get(0).get(1).get(1)).getText().contains(report2_line) }
                     }
                 },
-                { assert snapshot(path(process.out.versions.get(0)).yaml).match() },
+                { assert snapshot(process.out.versions_trim_galore).match() },
             )
         }
     }
@@ -152,7 +151,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    path(process.out.versions.get(0)).yaml,
+                    process.out.versions_trim_galore,
                     process.out.reads,
                     process.out.unpaired
                 ).match() },
@@ -181,7 +180,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(process.out).match() },
-                { assert snapshot(path(process.out.versions.get(0)).yaml).match("versions") },
+                { assert snapshot(process.out.versions_trim_galore).match("versions") }
             )
         }
     }