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Merged
nvnieuwk merged 3 commits into from
Oct 29, 2025
Merged

topics bismark/align #9272

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c393af9
topics bismark/align
nvnieuwk Oct 28, 2025
f66cf41
fix versions command
nvnieuwk Oct 28, 2025
40cea16
Merge branch 'master' into topics/bismarck-align
mribeirodantas Oct 29, 2025
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12 changes: 1 addition & 11 deletions modules/nf-core/bismark/align/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ process BISMARK_ALIGN {
tuple val(meta), path("*bam") , emit: bam
tuple val(meta), path("*report.txt"), emit: report
tuple val(meta), path("*fq.gz") , emit: unmapped, optional: true
path "versions.yml" , emit: versions
tuple val("${task.process}"), val("bismark"), eval('bismark --version | grep Version | sed -e "s/Bismark Version: v//" | xargs'), topic: versions, emit: versions_bismark

when:
task.ext.when == null || task.ext.when
Expand Down Expand Up @@ -61,11 +61,6 @@ process BISMARK_ALIGN {
--genome ${index} \\
--bam \\
${args}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
END_VERSIONS
"""

stub:
Expand All @@ -74,10 +69,5 @@ process BISMARK_ALIGN {
"""
touch ${prefix}.bam
touch ${prefix}.report.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
END_VERSIONS
"""
}
28 changes: 21 additions & 7 deletions modules/nf-core/bismark/align/meta.yml
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Expand Up @@ -85,13 +85,27 @@ output:
description: Output FastQ file(s) containing unmapped reads
pattern: "*.{fq.gz}"
ontologies: []
versions:
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"
ontologies:
- edam: http://edamontology.org/format_3750 # YAML
versions_bismark:
- - ${task.process}:
type: string
description: The process the versions were collected from
- bismark:
type: string
description: The tool name
- 'bismark --version | grep Version | sed -e "s/Bismark Version: v//" | xargs':
type: string
description: The version of the tool
topics:
- versions:
- - process:
type: string
description: The process the versions were collected from
- tool:
type: string
description: The tool name
- version:
type: string
description: The version of the tool
authors:
- "@phue"
maintainers:
Expand Down
15 changes: 5 additions & 10 deletions modules/nf-core/bismark/align/tests/main.nf.test
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Expand Up @@ -53,8 +53,7 @@ nextflow_process {
bam(process.out.bam[0][1]).getReadsMD5(),
file(process.out.report[0][1]).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5009"),
process.out.unmapped,
process.out.versions,
path(process.out.versions[0]).yaml
process.out.findAll { key, val -> key.startsWith('versions') },
).match()
}
)
Expand Down Expand Up @@ -92,8 +91,7 @@ nextflow_process {
bam(process.out.bam[0][1]).getReadsMD5(),
file(process.out.report[0][1]).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5009"),
process.out.unmapped,
process.out.versions,
path(process.out.versions[0]).yaml
process.out.findAll { key, val -> key.startsWith('versions') },
).match()
}
)
Expand Down Expand Up @@ -128,8 +126,7 @@ nextflow_process {
bam(process.out.bam[0][1]).getReadsMD5(),
file(process.out.report[0][1]).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5009"),
process.out.unmapped,
process.out.versions,
path(process.out.versions[0]).yaml
process.out.findAll { key, val -> key.startsWith('versions') },
).match()
}
)
Expand Down Expand Up @@ -167,8 +164,7 @@ nextflow_process {
bam(process.out.bam[0][1]).getReadsMD5(),
file(process.out.report[0][1]).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5009"),
process.out.unmapped,
process.out.versions,
path(process.out.versions[0]).yaml
process.out.findAll { key, val -> key.startsWith('versions') },
).match()
}
)
Expand Down Expand Up @@ -203,8 +199,7 @@ nextflow_process {
bam(process.out.bam[0][1]).getReadsMD5(),
file(process.out.report[0][1]).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5047"),
process.out.unmapped,
process.out.versions,
path(process.out.versions[0]).yaml
process.out.findAll { key, val -> key.startsWith('versions') },
).match()
}
)
Expand Down
85 changes: 45 additions & 40 deletions modules/nf-core/bismark/align/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -5,108 +5,113 @@
true,
[

],
[
"versions.yml:md5,72777174718c419301be78c0840f1931"
],
{
"BISMARK_ALIGN": {
"bismark": "0.25.1"
}
"versions_bismark": [
[
"BISMARK_ALIGN",
"bismark",
"0.25.1"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nextflow": "25.10.0"
},
"timestamp": "2025-09-26T12:09:08.59445088"
"timestamp": "2025-10-28T15:31:46.994204006"
},
"hisat2 | paired-end | sarscov2 genome [fasta]": {
"content": [
"fb9d284aec4b2c727af3c5ffd77c6381",
false,
[

],
[
"versions.yml:md5,72777174718c419301be78c0840f1931"
],
{
"BISMARK_ALIGN": {
"bismark": "0.25.1"
}
"versions_bismark": [
[
"BISMARK_ALIGN",
"bismark",
"0.25.1"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nextflow": "25.10.0"
},
"timestamp": "2025-09-26T12:08:47.207193467"
"timestamp": "2025-10-28T15:31:21.888003798"
},
"bowtie2 | paired-end | sarscov2 genome [fasta]": {
"content": [
"458c5350c3f96a8dde710985bfb62827",
false,
[

],
[
"versions.yml:md5,72777174718c419301be78c0840f1931"
],
{
"BISMARK_ALIGN": {
"bismark": "0.25.1"
}
"versions_bismark": [
[
"BISMARK_ALIGN",
"bismark",
"0.25.1"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nextflow": "25.10.0"
},
"timestamp": "2025-09-26T12:08:02.040747075"
"timestamp": "2025-10-28T15:30:37.313541027"
},
"bowtie2 | single-end | sarscov2 genome [fasta]": {
"content": [
"936c0d5ce713130113e99e09a5b53afd",
true,
[

],
[
"versions.yml:md5,72777174718c419301be78c0840f1931"
],
{
"BISMARK_ALIGN": {
"bismark": "0.25.1"
}
"versions_bismark": [
[
"BISMARK_ALIGN",
"bismark",
"0.25.1"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nextflow": "25.10.0"
},
"timestamp": "2025-09-26T12:07:37.985126432"
"timestamp": "2025-10-28T15:30:15.340678938"
},
"hisat2 | single-end | sarscov2 genome [fasta]": {
"content": [
"936c0d5ce713130113e99e09a5b53afd",
true,
[

],
[
"versions.yml:md5,72777174718c419301be78c0840f1931"
],
{
"BISMARK_ALIGN": {
"bismark": "0.25.1"
}
"versions_bismark": [
[
"BISMARK_ALIGN",
"bismark",
"0.25.1"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nextflow": "25.10.0"
},
"timestamp": "2025-09-26T12:08:24.007957857"
"timestamp": "2025-10-28T15:30:58.182901875"
}
}
1 change: 0 additions & 1 deletion subworkflows/nf-core/fastq_align_dedup_bismark/main.nf
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Expand Up @@ -42,7 +42,6 @@ workflow FASTQ_ALIGN_DEDUP_BISMARK {
)
ch_alignments = BISMARK_ALIGN.out.bam
ch_alignment_reports = BISMARK_ALIGN.out.report.map{ meta, report -> [ meta, report, [] ] }
ch_versions = ch_versions.mix(BISMARK_ALIGN.out.versions)

if (!skip_deduplication) {
/*
Expand Down
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