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nvnieuwk wants to merge 5 commits into from
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POC: topics #9159

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8d95f7c
POC topic versions
nvnieuwk Sep 30, 2025
6f53cbb
update test snaps
nvnieuwk Sep 30, 2025
48455e8
update meta.yml
nvnieuwk Sep 30, 2025
869d805
add topics to meta yaml
nvnieuwk Oct 1, 2025
0a6c97b
update meta yml
nvnieuwk Oct 28, 2025
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12 changes: 1 addition & 11 deletions modules/nf-core/bwamem2/index/main.nf
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Expand Up @@ -14,7 +14,7 @@ process BWAMEM2_INDEX {

output:
tuple val(meta), path("bwamem2"), emit: index
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('bwa-mem2'), eval("bwa-mem2 version 2>&1 | tail -1"), topic: versions, emit: versions1
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@mirpedrol mirpedrol Oct 1, 2025

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Just to be picky here, but the harshil alignment is not correct 😂


when:
task.ext.when == null || task.ext.when
Expand All @@ -29,11 +29,6 @@ process BWAMEM2_INDEX {
$args \\
-p bwamem2/${prefix} \\
$fasta

cat <<-END_VERSIONS > versions.yml
"${task.process}":
bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
END_VERSIONS
"""

stub:
Expand All @@ -46,10 +41,5 @@ process BWAMEM2_INDEX {
touch bwamem2/${prefix}.pac
touch bwamem2/${prefix}.amb
touch bwamem2/${prefix}.bwt.2bit.64

cat <<-END_VERSIONS > versions.yml
"${task.process}":
bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
END_VERSIONS
"""
}
28 changes: 21 additions & 7 deletions modules/nf-core/bwamem2/index/meta.yml
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Expand Up @@ -39,13 +39,27 @@ output:
pattern: "*.{0123,amb,ann,bwt.2bit.64,pac}"
ontologies:
- edam: "http://edamontology.org/data_3210" # Genome index
versions:
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"
ontologies:
- edam: http://edamontology.org/format_3750 # YAML
versions1:
- - ${task.process}:
type: string
description: The process the versions were collected from
- bwa-mem2:
type: string
description: The tool name
- bwa-mem2 version 2>&1 | tail -1:
type: string
description: The command used to generate 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
Comment on lines +54 to +62
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@mirpedrol mirpedrol Oct 3, 2025

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this looks good!
but if we want to automate it somehow, the values of the topic channel should be the same that we add for versions1: ${task.process}, bwa-mem2 and bwa-mem2 version 2>&1 | tail -1.
It doesn't look as nice, but it's the only way we can automate the generation of the meta.yml

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@nvnieuwk nvnieuwk Oct 3, 2025

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Thanks the main issue here is that the versions topic can consist of multiple tools here. I'm also not sure this needs automation as this will be in the template anyways. I've tried adding the automation, but it's not that trivial to do :/

authors:
- "@maxulysse"
maintainers:
Expand Down
12 changes: 2 additions & 10 deletions modules/nf-core/bwamem2/index/tests/main.nf.test
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Expand Up @@ -24,11 +24,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.index,
process.out.versions,
path(process.out.versions[0]).yaml
).match() }
{ assert snapshot(process.out).match() }
)
}
}
Expand All @@ -51,11 +47,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.index,
process.out.versions,
path(process.out.versions[0]).yaml
).match() }
{ assert snapshot(process.out).match() }
)
}
}
Expand Down
120 changes: 82 additions & 38 deletions modules/nf-core/bwamem2/index/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,64 +1,108 @@
{
"fasta - stub": {
"content": [
[
[
{
"id": "test"
},
{
"0": [
[
{
"id": "test"
},
[
"genome.fasta.0123:md5,d41d8cd98f00b204e9800998ecf8427e",
"genome.fasta.amb:md5,d41d8cd98f00b204e9800998ecf8427e",
"genome.fasta.ann:md5,d41d8cd98f00b204e9800998ecf8427e",
"genome.fasta.bwt.2bit.64:md5,d41d8cd98f00b204e9800998ecf8427e",
"genome.fasta.pac:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
],
"1": [
[
"BWAMEM2_INDEX",
"bwa-mem2",
"2.2.1"
]
],
"index": [
[
{
"id": "test"
},
[
"genome.fasta.0123:md5,d41d8cd98f00b204e9800998ecf8427e",
"genome.fasta.amb:md5,d41d8cd98f00b204e9800998ecf8427e",
"genome.fasta.ann:md5,d41d8cd98f00b204e9800998ecf8427e",
"genome.fasta.bwt.2bit.64:md5,d41d8cd98f00b204e9800998ecf8427e",
"genome.fasta.pac:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
],
"versions1": [
[
"genome.fasta.0123:md5,d41d8cd98f00b204e9800998ecf8427e",
"genome.fasta.amb:md5,d41d8cd98f00b204e9800998ecf8427e",
"genome.fasta.ann:md5,d41d8cd98f00b204e9800998ecf8427e",
"genome.fasta.bwt.2bit.64:md5,d41d8cd98f00b204e9800998ecf8427e",
"genome.fasta.pac:md5,d41d8cd98f00b204e9800998ecf8427e"
"BWAMEM2_INDEX",
"bwa-mem2",
"2.2.1"
]
]
],
[
"versions.yml:md5,9ffd13d12e7108ed15c58566bc4717d6"
],
{
"BWAMEM2_INDEX": {
"bwamem2": "2.2.1"
}
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
},
"timestamp": "2025-09-04T08:55:53.219699135"
"timestamp": "2025-09-30T15:48:12.646279004"
},
"fasta": {
"content": [
[
[
{
"id": "test"
},
{
"0": [
[
{
"id": "test"
},
[
"genome.fasta.0123:md5,b02870de80106104abcb03cd9463e7d8",
"genome.fasta.amb:md5,3a68b8b2287e07dd3f5f95f4344ba76e",
"genome.fasta.ann:md5,c32e11f6c859f166c7525a9c1d583567",
"genome.fasta.bwt.2bit.64:md5,d097a1b82dee375d41a1ea69895a9216",
"genome.fasta.pac:md5,983e3d2cd6f36e2546e6d25a0da78d66"
]
]
],
"1": [
[
"BWAMEM2_INDEX",
"bwa-mem2",
"2.2.1"
]
],
"index": [
[
{
"id": "test"
},
[
"genome.fasta.0123:md5,b02870de80106104abcb03cd9463e7d8",
"genome.fasta.amb:md5,3a68b8b2287e07dd3f5f95f4344ba76e",
"genome.fasta.ann:md5,c32e11f6c859f166c7525a9c1d583567",
"genome.fasta.bwt.2bit.64:md5,d097a1b82dee375d41a1ea69895a9216",
"genome.fasta.pac:md5,983e3d2cd6f36e2546e6d25a0da78d66"
]
]
],
"versions1": [
[
"genome.fasta.0123:md5,b02870de80106104abcb03cd9463e7d8",
"genome.fasta.amb:md5,3a68b8b2287e07dd3f5f95f4344ba76e",
"genome.fasta.ann:md5,c32e11f6c859f166c7525a9c1d583567",
"genome.fasta.bwt.2bit.64:md5,d097a1b82dee375d41a1ea69895a9216",
"genome.fasta.pac:md5,983e3d2cd6f36e2546e6d25a0da78d66"
"BWAMEM2_INDEX",
"bwa-mem2",
"2.2.1"
]
]
],
[
"versions.yml:md5,9ffd13d12e7108ed15c58566bc4717d6"
],
{
"BWAMEM2_INDEX": {
"bwamem2": "2.2.1"
}
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
},
"timestamp": "2025-09-04T08:55:45.007921901"
"timestamp": "2025-09-30T15:48:02.557291528"
}
}
15 changes: 2 additions & 13 deletions modules/nf-core/bwamem2/mem/main.nf
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Expand Up @@ -19,7 +19,8 @@ process BWAMEM2_MEM {
tuple val(meta), path("*.cram") , emit: cram, optional:true
tuple val(meta), path("*.crai") , emit: crai, optional:true
tuple val(meta), path("*.csi") , emit: csi , optional:true
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('bwa-mem2'), eval("bwa-mem2 version 2>&1 | tail -1"), topic: versions, emit: versions_bwamem2
tuple val("${task.process}"), val('samtools'), eval("samtools --version 2>&1 | head -1 | sed 's/^.*samtools //'"), topic: versions, emit: versions_samtools

when:
task.ext.when == null || task.ext.when
Expand All @@ -46,12 +47,6 @@ process BWAMEM2_MEM {
\$INDEX \\
$reads \\
| samtools $samtools_command $args2 -@ $task.cpus ${reference} -o ${prefix}.${extension} -

cat <<-END_VERSIONS > versions.yml
"${task.process}":
bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""

stub:
Expand All @@ -73,11 +68,5 @@ process BWAMEM2_MEM {
"""
touch ${prefix}.${extension}
${create_index}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}
39 changes: 32 additions & 7 deletions modules/nf-core/bwamem2/mem/meta.yml
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@@ -1,3 +1,4 @@
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
name: bwamem2_mem
description: Performs fastq alignment to a fasta reference using BWA
keywords:
Expand Down Expand Up @@ -118,13 +119,37 @@ output:
description: Index file for BAM file
pattern: "*.{csi}"
ontologies: []
versions:
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"
ontologies:
- edam: http://edamontology.org/format_3750 # YAML
versions_bwamem2:
- - ${task.process}:
type: string
description: The process the versions were collected from
- bwa-mem2:
type: string
description: The tool name
- bwa-mem2 version 2>&1 | tail -1:
type: string
description: The command used to generate the version of the tool
versions_samtools:
- - ${task.process}:
type: string
description: The process the versions were collected from
- samtools:
type: string
description: The tool name
- samtools --version 2>&1 | head -1 | sed 's/^.*samtools //':
type: string
description: The command used to generate 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:
- "@maxulysse"
- "@matthdsm"
Expand Down
8 changes: 4 additions & 4 deletions modules/nf-core/bwamem2/mem/tests/main.nf.test
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Expand Up @@ -46,7 +46,7 @@ nextflow_process {
{ assert snapshot(
bam(process.out.bam[0][1]).getHeaderMD5(),
bam(process.out.bam[0][1]).getReadsMD5(),
process.out.versions
process.out.findAll { key, val -> key.startsWith("versions") }
).match() }
)
}
Expand Down Expand Up @@ -75,7 +75,7 @@ nextflow_process {
{ assert snapshot(
bam(process.out.bam[0][1]).getHeaderMD5(),
bam(process.out.bam[0][1]).getReadsMD5(),
process.out.versions
process.out.findAll { key, val -> key.startsWith("versions") }
).match() }
)
}
Expand Down Expand Up @@ -107,7 +107,7 @@ nextflow_process {
{ assert snapshot(
bam(process.out.bam[0][1]).getHeaderMD5(),
bam(process.out.bam[0][1]).getReadsMD5(),
process.out.versions
process.out.findAll { key, val -> key.startsWith("versions") }
).match() }
)
}
Expand Down Expand Up @@ -139,7 +139,7 @@ nextflow_process {
{ assert snapshot(
bam(process.out.bam[0][1]).getHeaderMD5(),
bam(process.out.bam[0][1]).getReadsMD5(),
process.out.versions
process.out.findAll { key, val -> key.startsWith("versions") }
).match() }
)
}
Expand Down
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