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fix(trimgalore): clean stale outputs on same-workdir retry #11308

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Merged
pinin4fjords merged 3 commits into from
Apr 26, 2026
Merged

fix(trimgalore): clean stale outputs on same-workdir retry #11308

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7315432
fix(trimgalore): clean stale outputs on same-workdir retry
pinin4fjords Apr 25, 2026
d9fc618
fix(trimgalore): pin cutadapt and python in env.yml to match docker
pinin4fjords Apr 25, 2026
5bb02b7
test(trimgalore): drop python pin, filter python version from snapshot
pinin4fjords Apr 25, 2026
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1 change: 1 addition & 0 deletions modules/nf-core/trimgalore/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,3 +5,4 @@ channels:
- bioconda
dependencies:
- bioconda::trim-galore=0.6.10
- bioconda::cutadapt=5.2
6 changes: 6 additions & 0 deletions modules/nf-core/trimgalore/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,9 @@ process TRIMGALORE {
def args_list = args.split("\\s(?=--)").toList()
args_list.removeAll { arg -> arg.toLowerCase().contains('_r2 ') }
"""
# Remove any trim_galore outputs left behind by a previous attempt that
# ran in this same workdir (e.g. AWS Batch retry after a Spot reclaim).
rm -f *.fq.gz *.html *.zip *_trimming_report.txt
[ ! -f ${prefix}.fastq.gz ] && ln -s ${reads} ${prefix}.fastq.gz
trim_galore \\
${args_list.join(' ')} \\
Expand All @@ -56,6 +59,9 @@ process TRIMGALORE {
}
else {
"""
# Remove any trim_galore outputs left behind by a previous attempt that
# ran in this same workdir (e.g. AWS Batch retry after a Spot reclaim).
rm -f *.fq.gz *.html *.zip *_trimming_report.txt
[ ! -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 Down
10 changes: 5 additions & 5 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 @@ -27,7 +27,7 @@ nextflow_process {
{ assert snapshot(
process.out.reads,
file(process.out.log[0][1]).readLines()[0..9], // line 11 changes
file(process.out.log[0][1]).readLines()[11..59],
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")}
).match() }
)
Expand Down Expand Up @@ -56,9 +56,9 @@ nextflow_process {
process.out.reads[0][1][0],
process.out.reads[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],
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
file(process.out.log[0][1][1]).readLines()[11..60],
file(process.out.log[0][1][1]).readLines()[11..60].findAll { !it.startsWith("This is cutadapt") }, // strip python version
process.out.findAll { key, val -> key.startsWith("versions")}
).match() }
)
Expand Down Expand Up @@ -95,9 +95,9 @@ nextflow_process {
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
file(process.out.log[0][1][0]).readLines()[11..59],
file(process.out.log[0][1][0]).readLines()[11..59].findAll { !it.startsWith("This is cutadapt") }, // strip python version
file(process.out.log[0][1][1]).readLines()[0..9], // line 11 changes
file(process.out.log[0][1][1]).readLines()[11..63],
file(process.out.log[0][1][1]).readLines()[11..63].findAll { !it.startsWith("This is cutadapt") }, // strip python version
process.out.findAll { key, val -> key.startsWith("versions")}
).match() }
)
Expand Down
5 changes: 0 additions & 5 deletions modules/nf-core/trimgalore/tests/main.nf.test.snap
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Expand Up @@ -70,7 +70,6 @@
"Output file will be GZIP compressed",
"",
"",
"This is cutadapt 5.2 with Python 3.12.12",
"Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC test_1.fastq.gz",
"Processing single-end reads on 1 core ...",
"",
Expand Down Expand Up @@ -133,7 +132,6 @@
"Output file will be GZIP compressed",
"",
"",
"This is cutadapt 5.2 with Python 3.12.12",
"Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC test_2.fastq.gz",
"Processing single-end reads on 1 core ...",
"",
Expand Down Expand Up @@ -254,7 +252,6 @@
"Output file will be GZIP compressed",
"",
"",
"This is cutadapt 5.2 with Python 3.12.12",
"Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC test_1.fastq.gz",
"Processing single-end reads on 1 core ...",
"",
Expand Down Expand Up @@ -316,7 +313,6 @@
"Output file will be GZIP compressed",
"",
"",
"This is cutadapt 5.2 with Python 3.12.12",
"Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC test_2.fastq.gz",
"Processing single-end reads on 1 core ...",
"",
Expand Down Expand Up @@ -407,7 +403,6 @@
"Output file will be GZIP compressed",
"",
"",
"This is cutadapt 5.2 with Python 3.12.12",
"Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC test.fastq.gz",
"Processing single-end reads on 1 core ...",
"",
Expand Down
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