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Merged
SPPearce merged 6 commits into from
Jan 6, 2026
Merged

Swap picard/collecthsmetrics to topic #9614

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5b00540
Swap picard/collecthsmetrics to topic
SPPearce Dec 31, 2025
8d1210e
Fix sed command
SPPearce Jan 5, 2026
ac417fa
Update snapshot
SPPearce Jan 6, 2026
1f0cc39
Update subworkflow too
SPPearce Jan 6, 2026
3ad59ae
Apply suggestions from code review
SPPearce Jan 6, 2026
93577b9
Merge branch 'master' into picard_metrics_topic
SPPearce Jan 6, 2026
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12 changes: 1 addition & 11 deletions modules/nf-core/picard/collecthsmetrics/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ process PICARD_COLLECTHSMETRICS {

output:
tuple val(meta), path("*_metrics") , emit: metrics
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('picard'), eval("picard CollectHsMetrics --version 2>&1 | sed -n 's/^Version:*//p'"), topic: versions, emit: versions_picard

when:
task.ext.when == null || task.ext.when
Expand Down Expand Up @@ -63,21 +63,11 @@ process PICARD_COLLECTHSMETRICS {
--INPUT $bam \\
--OUTPUT ${prefix}.CollectHsMetrics.coverage_metrics


cat <<-END_VERSIONS > versions.yml
"${task.process}":
picard: \$(echo \$(picard CollectHsMetrics --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.CollectHsMetrics.coverage_metrics

cat <<-END_VERSIONS > versions.yml
"${task.process}":
picard: \$(echo \$(picard CollectHsMetrics --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
}
27 changes: 21 additions & 6 deletions modules/nf-core/picard/collecthsmetrics/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -99,13 +99,28 @@ output:
description: Alignment metrics files generated by picard
pattern: "*_{metrics}"
ontologies: []
versions_picard:
- - ${task.process}:
type: string
description: The process the versions were collected from
- picard:
type: string
description: The tool name
- "picard CollectHsMetrics --version 2>&1 | sed -n 's/^Version:*//p'":
type: string
description: The command used to generate the version of the tool

topics:
versions:
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"
ontologies:
- edam: http://edamontology.org/format_3750 # YAML
- - ${task.process}:
type: string
description: The process the versions were collected from
- picard:
type: string
description: The tool name
- "picard CollectHsMetrics --version 2>&1 | sed -n 's/^Version:*//p'":
type: string
description: The command used to generate the version of the tool
authors:
- "@projectoriented"
- "@matthdsm"
Expand Down
12 changes: 6 additions & 6 deletions modules/nf-core/picard/collecthsmetrics/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@ nextflow_process {
file(process.out.metrics[0][1]).name,
size,
lines,
process.out.versions
process.out.findAll { key, val -> key.startsWith("versions") }
).match()
}
)
Expand Down Expand Up @@ -77,7 +77,7 @@ nextflow_process {
file(process.out.metrics[0][1]).name,
size,
lines,
process.out.versions
process.out.findAll { key, val -> key.startsWith("versions") }
).match()
}
)
Expand Down Expand Up @@ -110,7 +110,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out.versions).match("versions") }
{ assert snapshot(process.out).match() }
)
}

Expand Down Expand Up @@ -146,7 +146,7 @@ nextflow_process {
file(process.out.metrics[0][1]).name,
size,
lines,
process.out.versions
process.out.findAll { key, val -> key.startsWith("versions") }
).match()
}
)
Expand Down Expand Up @@ -185,7 +185,7 @@ nextflow_process {
file(process.out.metrics[0][1]).name,
size,
lines,
process.out.versions
process.out.findAll { key, val -> key.startsWith("versions") }
).match()
}
)
Expand Down Expand Up @@ -224,7 +224,7 @@ nextflow_process {
file(process.out.metrics[0][1]).name,
size,
lines,
process.out.versions
process.out.findAll { key, val -> key.startsWith("versions") }
).match()
}
)
Expand Down
145 changes: 103 additions & 42 deletions modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -105,15 +105,64 @@
"88\t0\t0",
"89\t0\t0"
],
[
"versions.yml:md5,533cf1e35d36fdacbb762f5df2e1b322"
]
{
"versions_picard": [
[
"PICARD_COLLECTHSMETRICS",
"picard",
"3.4.0"
]
]
}
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2026-01-05T17:03:29.566021877"
},
"sarscov2 - bam - stub": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
"test.CollectHsMetrics.coverage_metrics:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
[
"PICARD_COLLECTHSMETRICS",
"picard",
"3.4.0"
]
],
"metrics": [
[
{
"id": "test",
"single_end": false
},
"test.CollectHsMetrics.coverage_metrics:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions_picard": [
[
"PICARD_COLLECTHSMETRICS",
"picard",
"3.4.0"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.7"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-09-15T10:37:59.62099935"
"timestamp": "2026-01-05T17:03:13.333276975"
},
"sarscov2 - bam - gzippedfa": {
"content": [
Expand Down Expand Up @@ -221,27 +270,21 @@
"88\t0\t0",
"89\t0\t0"
],
[
"versions.yml:md5,533cf1e35d36fdacbb762f5df2e1b322"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.7"
},
"timestamp": "2025-09-15T10:37:32.831030701"
},
"versions": {
"content": [
[
"versions.yml:md5,533cf1e35d36fdacbb762f5df2e1b322"
]
{
"versions_picard": [
[
"PICARD_COLLECTHSMETRICS",
"picard",
"3.4.0"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.7"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-09-15T10:37:42.492104283"
"timestamp": "2026-01-05T17:03:04.382110367"
},
"sarscov2 - bam - samebed": {
"content": [
Expand Down Expand Up @@ -349,15 +392,21 @@
"88\t0\t0",
"89\t0\t0"
],
[
"versions.yml:md5,533cf1e35d36fdacbb762f5df2e1b322"
]
{
"versions_picard": [
[
"PICARD_COLLECTHSMETRICS",
"picard",
"3.4.0"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.7"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-09-15T10:38:39.302597954"
"timestamp": "2026-01-05T17:13:22.872920293"
},
"sarscov2 - bam": {
"content": [
Expand Down Expand Up @@ -465,15 +514,21 @@
"88\t0\t0",
"89\t0\t0"
],
[
"versions.yml:md5,533cf1e35d36fdacbb762f5df2e1b322"
]
{
"versions_picard": [
[
"PICARD_COLLECTHSMETRICS",
"picard",
"3.4.0"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.7"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-09-15T10:37:15.861292725"
"timestamp": "2026-01-05T17:02:47.615784738"
},
"sarscov2 - bam - bed": {
"content": [
Expand Down Expand Up @@ -581,14 +636,20 @@
"88\t0\t0",
"89\t0\t0"
],
[
"versions.yml:md5,533cf1e35d36fdacbb762f5df2e1b322"
]
{
"versions_picard": [
[
"PICARD_COLLECTHSMETRICS",
"picard",
"3.4.0"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.7"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-09-15T10:38:18.912909604"
"timestamp": "2026-01-05T17:13:02.812282052"
}
}
19 changes: 10 additions & 9 deletions subworkflows/nf-core/bam_qc_picard/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -15,27 +15,28 @@ workflow BAM_QC_PICARD {
ch_fasta_gzi // channel: [ val(meta), fasta_gzi ]

main:
ch_versions = Channel.empty()
ch_coverage_metrics = Channel.empty()
ch_versions = channel.empty()
ch_coverage_metrics = channel.empty()

ch_bam_bai = ch_bam_bai_bait_target.map{meta, bam, bai, bait, target -> return [meta,bam,bai]}
ch_bam_bai = ch_bam_bai_bait_target.map{meta, bam, bai, _bait, _target -> return [meta,bam,bai]}

PICARD_COLLECTMULTIPLEMETRICS( ch_bam_bai, ch_fasta, ch_fasta_fai )
ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions)

ch_bam_bai_bait_target_branched = ch_bam_bai_bait_target.branch {
hsmetrics : it.size == 5 && it[3] != [] && it[4] != []
return it
meta, bam, bai, bait, target ->
hsmetrics : bait != [] && target != []
return [ meta, bam, bai, bait, target ]
wgsmetrics : true
return [ it[0], it[1], it[2] ]
return [ meta, bam, bai ]
}

PICARD_COLLECTHSMETRICS( ch_bam_bai_bait_target_branched.hsmetrics, ch_fasta, ch_fasta_fai, ch_fasta_dict, ch_fasta_gzi )
ch_coverage_metrics = ch_coverage_metrics.mix(PICARD_COLLECTHSMETRICS.out.metrics)
ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())
// PICARD_COLLECTHSMETRICS emits version as a topic channel

PICARD_COLLECTWGSMETRICS( ch_bam_bai_bait_target_branched.wgsmetrics, ch_fasta, ch_fasta_fai, [] )
ch_versions = ch_versions.mix(PICARD_COLLECTWGSMETRICS.out.versions.first())
ch_versions = ch_versions.mix(PICARD_COLLECTWGSMETRICS.out.versions)
ch_coverage_metrics = ch_coverage_metrics.mix(PICARD_COLLECTWGSMETRICS.out.metrics)

emit:
Expand Down
9 changes: 4 additions & 5 deletions subworkflows/nf-core/bam_qc_picard/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -57,15 +57,14 @@
"## htsjdk.samtools.metrics.StringHeader"
],
[
"versions.yml:md5,3b2235bbbda6df95419f3806503827d0",
"versions.yml:md5,720ecdeea54685db81f179f2f4e8e4ca"
"versions.yml:md5,3b2235bbbda6df95419f3806503827d0"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.7"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-09-15T10:39:19.027288405"
"timestamp": "2026-01-06T12:22:35.756653797"
},
"sascov2_wgs - [bam,bai]": {
"content": [
Expand Down
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