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Add pigz to trimgalore #7169

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merged 4 commits into from
Dec 6, 2024
Merged

Add pigz to trimgalore #7169

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8e2a01f
test(#6505): Add pigz to versions.yml
edmundmiller Dec 6, 2024
ed8a5c8
feat: Add pigz to trimgalore
edmundmiller Dec 6, 2024
461a57e
style: Run lsp format
edmundmiller Dec 6, 2024
73a7f77
Update modules/nf-core/trimgalore/main.nf
SPPearce Dec 6, 2024
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2 changes: 1 addition & 1 deletion modules/nf-core/trimgalore/environment.yml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::cutadapt=4.9
- bioconda::trim-galore=0.6.10
- conda-forge::pigz=2.8
49 changes: 30 additions & 19 deletions modules/nf-core/trimgalore/main.nf
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Original file line number Diff line number Diff line change
@@ -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
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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
Expand All @@ -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 \\
${prefix}_1.fastq.gz \\
Expand All @@ -69,6 +77,7 @@ process TRIMGALORE {
"${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
"""
}
Expand All @@ -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 > ${prefix}_2_trimmed.fq.gz ;"
Expand All @@ -91,6 +101,7 @@ process TRIMGALORE {
"${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
"""
}
14 changes: 9 additions & 5 deletions modules/nf-core/trimgalore/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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() },
)
}
}
Expand All @@ -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() },
)
}
}
Expand Down Expand Up @@ -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() },
)
}
}
Expand All @@ -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") },
)
}
}
}
}
75 changes: 53 additions & 22 deletions modules/nf-core/trimgalore/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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": [
Expand Down Expand Up @@ -42,7 +46,7 @@

],
"5": [
"versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50"
"versions.yml:md5,5928323d579768de37e83c56c821757f"
],
"html": [

Expand All @@ -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": [
Expand Down Expand Up @@ -119,7 +130,7 @@

],
"5": [
"versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50"
"versions.yml:md5,5928323d579768de37e83c56c821757f"
],
"html": [

Expand Down Expand Up @@ -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"
}
}
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