Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add pigz to trimgalore #7169

Merged
merged 4 commits into from
Dec 6, 2024
Merged

Add pigz to trimgalore #7169

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion modules/nf-core/trimgalore/environment.yml
View file
Open in desktop
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
View file
Open in desktop
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

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"
}
}
Loading
Loading