Add pigz to trimgalore (#7169)

* test(#6505): Add pigz to versions.yml * feat: Add pigz to trimgalore nf-core/atacseq#394 FelixKrueger/TrimGalore#16 (comment) https://github.com/FelixKrueger/TrimGalore/blob/master/CHANGELOG.md#version-060-release-on-1-mar-2019 * style: Run lsp format * Update modules/nf-core/trimgalore/main.nf --------- Co-authored-by: Simon Pearce <[email protected]>
nf-core · Dec 6, 2024 · 4c2d06a · 4c2d06a
1 parent a437c79
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diff --git a/modules/nf-core/trimgalore/environment.yml b/modules/nf-core/trimgalore/environment.yml
@@ -1,7 +1,7 @@
 channels:
   - conda-forge
   - bioconda
-
 dependencies:
   - bioconda::cutadapt=4.9
   - bioconda::trim-galore=0.6.10
+  - conda-forge::pigz=2.8
diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf
@@ -1,37 +1,43 @@
 process TRIMGALORE {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/trim-galore%3A0.6.10--hdfd78af_1' :
-        'biocontainers/trim-galore:0.6.10--hdfd78af_1' }"
+    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'}"
 
     input:
     tuple val(meta), path(reads)
 
     output:
     tuple val(meta), path("*{3prime,5prime,trimmed,val}*.fq.gz"), emit: reads
-    tuple val(meta), path("*report.txt")                        , emit: log     , optional: true
-    tuple val(meta), path("*unpaired*.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*.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
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
     // Calculate number of --cores for TrimGalore based on value of task.cpus
-    // See: https://github.com/FelixKrueger/TrimGalore/blob/master/Changelog.md#version-060-release-on-1-mar-2019
+    // See: https://github.com/FelixKrueger/TrimGalore/blob/master/CHANGELOG.md#version-060-release-on-1-mar-2019
     // See: https://github.com/nf-core/atacseq/pull/65
     def cores = 1
     if (task.cpus) {
         cores = (task.cpus as int) - 4
-        if (meta.single_end) cores = (task.cpus as int) - 3
-        if (cores < 1) cores = 1
-        if (cores > 8) cores = 8
+        if (meta.single_end) {
+            cores = (task.cpus as int) - 3
+        }
+        if (cores < 1) {
+            cores = 1
+        }
+        if (cores > 8) {
+            cores = 8
+        }
     }
 
     // Added soft-links to original fastqs for consistent naming in MultiQC
@@ -40,26 +46,28 @@ process TRIMGALORE {
         def args_list = args.split("\\s(?=--)").toList()
         args_list.removeAll { it.toLowerCase().contains('_r2 ') }
         """
-        [ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
+        [ ! -f  ${prefix}.fastq.gz ] && ln -s ${reads} ${prefix}.fastq.gz
         trim_galore \\
             ${args_list.join(' ')} \\
-            --cores $cores \\
+            --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 {
+    }
+    else {
         """
         [ ! -f  ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
         [ ! -f  ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
         trim_galore \\
-            $args \\
-            --cores $cores \\
+            ${args} \\
+            --cores ${cores} \\
             --paired \\
             --gzip \\
             ${prefix}_1.fastq.gz \\
@@ -69,6 +77,7 @@ process TRIMGALORE {
         "${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
         """
     }
@@ -78,7 +87,8 @@ process TRIMGALORE {
     if (meta.single_end) {
         output_command = "echo '' | gzip > ${prefix}_trimmed.fq.gz ;"
         output_command += "touch ${prefix}.fastq.gz_trimming_report.txt"
-    } else {
+    }
+    else {
         output_command = "echo '' | gzip > ${prefix}_1_trimmed.fq.gz ;"
         output_command += "touch ${prefix}_1.fastq.gz_trimming_report.txt ;"
         output_command += "echo '' | gzip > ${prefix}_2_trimmed.fq.gz ;"
@@ -91,6 +101,7 @@ process TRIMGALORE {
     "${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
     """
 }
diff --git a/modules/nf-core/trimgalore/tests/main.nf.test b/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(process.out.versions).match() }
+                { assert snapshot(path(process.out.versions.get(0)).yaml).match() },
             )
         }
     }
@@ -61,7 +61,10 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions.get(0)).yaml
+                ).match() },
             )
         }
     }
@@ -118,7 +121,7 @@ nextflow_process {
                     { assert path(process.out.log.get(0).get(1).get(1)).getText().contains(report2_line) }
                     }
                 },
-                { assert snapshot(process.out.versions).match() }
+                { assert snapshot(path(process.out.versions.get(0)).yaml).match() },
             )
         }
     }
@@ -143,8 +146,9 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(process.out).match() },
+                { assert snapshot(path(process.out.versions.get(0)).yaml).match("versions") },
             )
         }
     }
-}
+}
diff --git a/modules/nf-core/trimgalore/tests/main.nf.test.snap b/modules/nf-core/trimgalore/tests/main.nf.test.snap
@@ -1,15 +1,19 @@
 {
     "test_trimgalore_single_end": {
         "content": [
-            [
-                "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50"
-            ]
+            {
+                "TRIMGALORE": {
+                    "trimgalore": "0.6.10",
+                    "cutadapt": 4.9,
+                    "pigz": 2.8
+                }
+            }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-10-22T19:23:17.969056957"
+        "timestamp": "2024-12-05T22:56:18.454197"
     },
     "test_trimgalore_single_end - stub": {
         "content": [
@@ -42,7 +46,7 @@
 
                 ],
                 "5": [
-                    "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50"
+                    "versions.yml:md5,5928323d579768de37e83c56c821757f"
                 ],
                 "html": [
 
@@ -69,18 +73,25 @@
 
                 ],
                 "versions": [
-                    "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50"
+                    "versions.yml:md5,5928323d579768de37e83c56c821757f"
                 ],
                 "zip": [
 
                 ]
+            },
+            {
+                "TRIMGALORE": {
+                    "trimgalore": "0.6.10",
+                    "cutadapt": 4.9,
+                    "pigz": 2.8
+                }
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-10-22T19:23:28.617831159"
+        "timestamp": "2024-12-05T22:56:22.085472"
     },
     "test_trimgalore_paired_end - stub": {
         "content": [
@@ -119,7 +130,7 @@
 
                 ],
                 "5": [
-                    "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50"
+                    "versions.yml:md5,5928323d579768de37e83c56c821757f"
                 ],
                 "html": [
 
@@ -152,29 +163,49 @@
 
                 ],
                 "versions": [
-                    "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50"
+                    "versions.yml:md5,5928323d579768de37e83c56c821757f"
                 ],
                 "zip": [
 
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-05T22:44:33.751013"
+    },
+    "versions": {
+        "content": [
+            {
+                "TRIMGALORE": {
+                    "trimgalore": "0.6.10",
+                    "cutadapt": 4.9,
+                    "pigz": 2.8
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-10-22T19:23:51.539787731"
+        "timestamp": "2024-12-05T22:57:28.77107"
     },
     "test_trimgalore_paired_end": {
         "content": [
-            [
-                "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50"
-            ]
+            {
+                "TRIMGALORE": {
+                    "trimgalore": "0.6.10",
+                    "cutadapt": 4.9,
+                    "pigz": 2.8
+                }
+            }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-10-22T19:23:41.16485915"
+        "timestamp": "2024-12-05T22:56:27.019872"
     }
 }