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fix(trimgalore): split reads emit into reads_se / reads_pe (alternative) #11329

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fix(trimgalore): split reads emit into reads_se / reads_pe (alternative) #11329

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29 changes: 14 additions & 15 deletions modules/nf-core/trimgalore/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -11,11 +11,16 @@ process TRIMGALORE {
tuple val(meta), path(reads)

output:
tuple val(meta), path("*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz"), emit: reads
tuple val(meta), path("*report.txt") , emit: log , optional: true
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
// Two `reads_*` emits with positive-only patterns covering every trim_galore
// output mode (default trim, --hardtrim5, --hardtrim3). PE per-mate intermediates
// (`${prefix}_<N>_trimmed.fq.gz`) deliberately match neither pattern, so an
// incomplete unlink of those files on retry can't leak into either channel.
tuple val(meta), path("${prefix}{_trimmed,.*bp_3prime,.*bp_5prime}.fq.gz") , emit: reads_se, optional: true
tuple val(meta), path("${prefix}_*{_val_1,_val_2,bp_3prime,bp_5prime}.fq.gz") , emit: reads_pe, optional: true
tuple val(meta), path("*report.txt") , emit: log , optional: true
tuple val(meta), path("*unpaired{,_1,_2}.fq.gz") , emit: unpaired, optional: true
tuple val(meta), path("*.html") , emit: html , optional: true
tuple val(meta), path("*.zip") , emit: zip , optional: true
tuple val("${task.process}"), val("trimgalore"), eval('trim_galore --version | grep -Eo "[0-9]+(\\.[0-9]+)+"'), topic: versions, emit: versions_trimgalore

when:
Expand All @@ -41,13 +46,11 @@ process TRIMGALORE {
}

// Added soft-links to original fastqs for consistent naming in MultiQC
def prefix = task.ext.prefix ?: "${meta.id}"
prefix = task.ext.prefix ?: "${meta.id}"
if (meta.single_end) {
def args_list = args.split("\\s(?=--)").toList()
args_list.removeAll { arg -> arg.toLowerCase().contains('_r2 ') }
"""
# Drop any trim_galore output left over from an interrupted previous attempt.
rm -f ${prefix}_trimmed.fq.gz
[ ! -f ${prefix}.fastq.gz ] && ln -s ${reads} ${prefix}.fastq.gz
trim_galore \\
${args_list.join(' ')} \\
Expand All @@ -58,10 +61,6 @@ process TRIMGALORE {
}
else {
"""
# Drop the per-mate intermediates --paired writes before validate_paired_end_files
# unlinks them. An attempt interrupted between cutadapt and validation leaves these
# behind and the output glob then matches 3 fastqs instead of 2.
rm -f ${prefix}_1_trimmed.fq.gz ${prefix}_2_trimmed.fq.gz
[ ! -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 \\
Expand All @@ -75,15 +74,15 @@ process TRIMGALORE {
}

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
prefix = task.ext.prefix ?: "${meta.id}"
if (meta.single_end) {
output_command = "echo '' | gzip > ${prefix}_trimmed.fq.gz ;"
output_command += "touch ${prefix}.fastq.gz_trimming_report.txt"
}
else {
output_command = "echo '' | gzip > ${prefix}_1_trimmed.fq.gz ;"
output_command = "echo '' | gzip > ${prefix}_1_val_1.fq.gz ;"
output_command += "touch ${prefix}_1.fastq.gz_trimming_report.txt ;"
output_command += "echo '' | gzip > ${prefix}_2_trimmed.fq.gz ;"
output_command += "echo '' | gzip > ${prefix}_2_val_2.fq.gz ;"
output_command += "touch ${prefix}_2.fastq.gz_trimming_report.txt"
}
"""
Expand Down
28 changes: 24 additions & 4 deletions modules/nf-core/trimgalore/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -32,16 +32,36 @@ input:
ontologies:
- edam: "http://edamontology.org/format_1930" # FASTQ
output:
reads:
reads_se:
- - meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:true ]
- "${prefix}{_trimmed,.*bp_3prime,.*bp_5prime}.fq.gz":
type: file
description: |
Single-end trimmed reads. Brace alternatives cover trim_galore's
output modes: `_trimmed` (default), `.<N>bp_3prime` (--hardtrim3),
`.<N>bp_5prime` (--hardtrim5).
pattern: "${prefix}{_trimmed,.*bp_3prime,.*bp_5prime}.fq.gz"
ontologies:
- edam: "http://edamontology.org/format_1930" # FASTQ
- edam: http://edamontology.org/format_3989 # GZIP format
reads_pe:
- - meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- "*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz":
- "${prefix}_*{_val_1,_val_2,bp_3prime,bp_5prime}.fq.gz":
type: file
description: The trimmed/modified fastq reads
pattern: "*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz"
description: |
Paired-end trimmed reads. Brace alternatives cover trim_galore's
output modes: `_val_<N>` (default), `bp_3prime` (--hardtrim3),
`bp_5prime` (--hardtrim5). PE per-mate intermediates
(`${prefix}_<N>_trimmed.fq.gz`) deliberately do not match this glob.
pattern: "${prefix}_*{_val_1,_val_2,bp_3prime,bp_5prime}.fq.gz"
ontologies:
- edam: "http://edamontology.org/format_1930" # FASTQ
- edam: http://edamontology.org/format_3989 # GZIP format
Expand Down
14 changes: 7 additions & 7 deletions modules/nf-core/trimgalore/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ nextflow_process {
assertAll (
{ assert process.success },
{ assert snapshot(
process.out.reads,
process.out.reads_se,
file(process.out.log[0][1]).readLines()[0..9], // line 11 changes
file(process.out.log[0][1]).readLines()[11..59].findAll { !it.startsWith("This is cutadapt") }, // strip python version
process.out.findAll { key, val -> key.startsWith("versions")}
Expand Down Expand Up @@ -53,8 +53,8 @@ nextflow_process {
assertAll (
{ assert process.success },
{ assert snapshot(
process.out.reads[0][1][0],
process.out.reads[0][1][1],
process.out.reads_pe[0][1][0],
process.out.reads_pe[0][1][1],
file(process.out.log[0][1][0]).readLines()[0..9], // line 11 changes
file(process.out.log[0][1][0]).readLines()[11..58].findAll { !it.startsWith("This is cutadapt") }, // strip python version
file(process.out.log[0][1][1]).readLines()[0..9], // line 11 changes
Expand Down Expand Up @@ -90,8 +90,8 @@ nextflow_process {
assertAll (
{ assert process.success },
{ assert snapshot(
process.out.reads[0][1][0],
process.out.reads[0][1][1],
process.out.reads_pe[0][1][0],
process.out.reads_pe[0][1][1],
process.out.unpaired[0][1][0],
process.out.unpaired[0][1][1],
file(process.out.log[0][1][0]).readLines()[0..9], // line 11 changes
Expand Down Expand Up @@ -123,7 +123,7 @@ nextflow_process {
assertAll (
{ assert process.success },
{ assert snapshot(
process.out.reads,
process.out.reads_se,
process.out.log,
process.out.findAll { key, val -> key.startsWith("versions")}
).match() }
Expand Down Expand Up @@ -152,7 +152,7 @@ nextflow_process {
assertAll (
{ assert process.success },
{ assert snapshot(
process.out.reads,
process.out.reads_pe,
process.out.log,
process.out.findAll { key, val -> key.startsWith("versions")}
).match() }
Expand Down
8 changes: 4 additions & 4 deletions modules/nf-core/trimgalore/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -8,8 +8,8 @@
"single_end": false
},
[
"test_1_trimmed.fq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
"test_2_trimmed.fq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
"test_1_val_1.fq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
"test_2_val_2.fq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
]
],
Expand Down Expand Up @@ -37,9 +37,9 @@
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
"nextflow": "25.10.4"
},
"timestamp": "2025-12-15T14:40:14.896140126"
"timestamp": "2026-04-28T10:39:33.698447"
},
"sarscov2 - fastq - paired-end - keep-unpaired": {
"content": [
Expand Down
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