Update cutadapt

modules/nf-core/cutadapt/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::cutadapt=5.0
+  - bioconda::cutadapt=5.2

modules/nf-core/cutadapt/main.nf

@@ -3,17 +3,17 @@ process CUTADAPT {
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/17/1758869538eb8e658077cc14cd7a4e76fd9b6d73d3a68f85a70bf292e39e27c5/data' :
-        'community.wave.seqera.io/library/cutadapt:5.0--991bbd2e184b7014' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/cutadapt:5.2--py311haab0aaa_0' :
+        'biocontainers/cutadapt:5.2--py311haab0aaa_0'}"
 
     input:
     tuple val(meta), path(reads)
 
     output:
     tuple val(meta), path('*.trim.fastq.gz'), emit: reads
     tuple val(meta), path('*.log')          , emit: log
-    path "versions.yml"                     , emit: versions
+    tuple val("${task.process}"), val("cutadapt"), eval('cutadapt --version'), topic: versions, emit: versions_cutadapt
 
     when:
     task.ext.when == null || task.ext.when
@@ -24,28 +24,24 @@ process CUTADAPT {
     def trimmed  = meta.single_end ? "-o ${prefix}.trim.fastq.gz" : "-o ${prefix}_1.trim.fastq.gz -p ${prefix}_2.trim.fastq.gz"
     """
     cutadapt \\
-        -Z \\
         --cores $task.cpus \\
         $args \\
         $trimmed \\
         $reads \\
         > ${prefix}.cutadapt.log
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        cutadapt: \$(cutadapt --version)
-    END_VERSIONS
     """
 
     stub:
-    def prefix  = task.ext.prefix ?: "${meta.id}"
-    def trimmed = meta.single_end ? "${prefix}.trim.fastq.gz" : "${prefix}_1.trim.fastq.gz ${prefix}_2.trim.fastq.gz"
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    if (meta.single_end) {
+        output_command = "echo '' | gzip > ${prefix}.trim.fastq.gz ;"
+    }
+    else {
+        output_command  = "echo '' | gzip > ${prefix}_1.trim.fastq.gz ;"
+        output_command += "echo '' | gzip > ${prefix}_2.trim.fastq.gz ;"
+    }
     """
+    ${output_command}
     touch ${prefix}.cutadapt.log
-    touch ${trimmed}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        cutadapt: \$(cutadapt --version)
-    END_VERSIONS
     """
 }

modules/nf-core/cutadapt/meta.yml

@@ -1,18 +1,22 @@
 name: cutadapt
-description: Perform adapter/quality trimming on sequencing reads
+description: Removes adapter sequences from sequencing reads
 keywords:
+  - adapter
+  - primers
+  - poly-A tails
   - trimming
-  - adapter trimming
-  - adapters
-  - quality trimming
+  - fastq
 tools:
-  - cuatadapt:
+  - cutadapt:
       description: |
-        Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
-      documentation: https://cutadapt.readthedocs.io/en/stable/index.html
+        Cutadapt finds and removes adapter sequences, primers, poly-A tails
+        and other types of unwanted sequence from your high-throughput sequencing reads.
+      homepage: https://cutadapt.readthedocs.io/en/stable/index.html
+      documentation: https://github.com/marcelm/cutadapt
       doi: 10.14806/ej.17.1.200
       licence: ["MIT"]
       identifier: biotools:cutadapt
+
 input:
   - - meta:
         type: map
@@ -24,7 +28,9 @@ input:
         description: |
           List of input FastQ files of size 1 and 2 for single-end and paired-end data,
           respectively.
-        ontologies: []
+        pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
+        ontologies:
+          - edam: "http://edamontology.org/format_1930" # FASTQ
 output:
   reads:
     - - meta:
@@ -37,6 +43,7 @@ output:
           description: The trimmed/modified fastq reads
           pattern: "*fastq.gz"
           ontologies:
+            - edam: "http://edamontology.org/format_1930" # FASTQ
             - edam: http://edamontology.org/format_3989 # GZIP format
   log:
     - - meta:
@@ -46,19 +53,37 @@ output:
             e.g. [ id:'test', single_end:false ]
       - "*.log":
           type: file
-          description: cuatadapt log file
+          description: cutadapt log file
           pattern: "*cutadapt.log"
-          ontologies: []
+          ontologies:
+            - edam: "http://edamontology.org/format_2330" # Textual format
+  versions_cutadapt:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - cutadapt:
+          type: string
+          description: The name of the tool
+      - cutadapt --version:
+          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
+      - cutadapt:
+          type: string
+          description: The name of the tool
+      - cutadapt --version:
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@drpatelh"
   - "@kevinmenden"
 maintainers:
   - "@drpatelh"
   - "@kevinmenden"
+  - "@vagkaratzas"

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

@@ -3,16 +3,14 @@ nextflow_process {
     name "Test Process CUTADAPT"
     script "../main.nf"
     process "CUTADAPT"
+
     tag "modules"
     tag "modules_nfcore"
     tag "cutadapt"
 
-    test("sarscov2 Illumina single end [fastq]") {
+    test("sarscov2 - fastq - single-end") {
 
         when {
-            params {
-                outdir   = "$outputDir"
-            }
             process {
                 """
                 input[0] = [
@@ -28,20 +26,18 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert process.out.reads != null },
-                { assert process.out.reads.get(0).get(1) ==~ ".*.trim.fastq.gz" },
-                { assert snapshot(process.out.versions).match("versions_single_end") },
-                { assert snapshot(path(process.out.reads.get(0).get(1)).linesGzip[0]).match() }
+                { assert snapshot(
+                    process.out.reads,
+                    file(process.out.log[0][1]).readLines()[1..10], // python versions differ in the default conda env and container
+                    process.out.findAll { key, val -> key.startsWith("versions")}
+                ).match() }
             )
         }
     }
 
-    test("sarscov2 Illumina paired-end [fastq]") {
+    test("sarscov2 - fastq - paired-end") {
 
         when {
-            params {
-                outdir   = "$outputDir"
-            }
             process {
                 """
                 input[0] = [
@@ -58,11 +54,39 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert process.out.reads != null },
-                { assert process.out.reads.get(0).get(1).get(0) ==~ ".*.1.trim.fastq.gz" },
-                { assert process.out.reads.get(0).get(1).get(1) ==~ ".*.2.trim.fastq.gz" },
-                { assert snapshot(path(process.out.reads.get(0).get(1).get(1)).linesGzip[0]).match() },
-                { assert snapshot(process.out.versions).match("versions_paired_end") }
+                { assert snapshot(
+                    process.out.reads,
+                    file(process.out.log[0][1]).readLines()[1..14], // python versions differ in the default conda env and container
+                    process.out.findAll { key, val -> key.startsWith("versions")}
+                ).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - fastq - single-end - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id: 'test', single_end:true ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                    ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert snapshot(
+                    process.out.reads,
+                    process.out.log,
+                    process.out.findAll { key, val -> key.startsWith("versions")}
+                ).match() }
             )
         }
     }