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Update to topics chromap/chromap #11025

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c57c2f9
Update to topics
LouisLeNezet Mar 23, 2026
e0ad947
Update sbwf
LouisLeNezet Mar 23, 2026
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22 changes: 2 additions & 20 deletions modules/nf-core/chromap/chromap/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ process CHROMAP_CHROMAP {

input:
tuple val(meta), path(reads)
tuple val(meta2), path(fasta)
tuple val(meta2), path(fasta), path(fai)
tuple val(meta3), path(index)
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@maxulysse maxulysse Mar 24, 2026

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what is this index?

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@LouisLeNezet LouisLeNezet Mar 24, 2026

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Because the subworkflow provide it.
I could also do a .map{ } to remove it for this process call, but I find it cleaner to always have the fasta index with the fasta in the channels.
What do you think ?

path barcodes
path whitelist
Expand All @@ -21,7 +21,7 @@ process CHROMAP_CHROMAP {
tuple val(meta), path("*.bam") , optional:true, emit: bam
tuple val(meta), path("*.tagAlign.gz"), optional:true, emit: tagAlign
tuple val(meta), path("*.pairs.gz") , optional:true, emit: pairs
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('chromap'), eval("chromap --version 2>&1"), topic: versions, emit: versions_chromap

when:
task.ext.when == null || task.ext.when
Expand Down Expand Up @@ -65,12 +65,6 @@ process CHROMAP_CHROMAP {
-o ${prefix}.${file_extension}

$compression_cmds

cat <<-END_VERSIONS > versions.yml
"${task.process}":
chromap: \$(echo \$(chromap --version 2>&1))
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
} else {
"""
Expand All @@ -84,12 +78,6 @@ process CHROMAP_CHROMAP {
-o ${prefix}.${file_extension}

$compression_cmds

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

Expand All @@ -100,11 +88,5 @@ process CHROMAP_CHROMAP {
touch ${prefix}.bam
echo "" | gzip > ${prefix}.tagAlign.gz
echo "" | gzip > ${prefix}.pairs.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
chromap: \$(echo \$(chromap --version 2>&1))
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}
34 changes: 27 additions & 7 deletions modules/nf-core/chromap/chromap/meta.yml
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Expand Up @@ -20,7 +20,8 @@ tools:
homepage: https://github.com/haowenz/chromap
documentation: https://github.com/haowenz/chromap
tool_dev_url: https://github.com/haowenz/chromap
licence: ["GPL v3"]
licence:
- "GPL v3"
identifier: ""
input:
- - meta:
Expand All @@ -44,6 +45,11 @@ input:
description: |
The fasta reference file.
ontologies: []
- fai:
type: file
description: |
The fasta reference file index.
ontologies: []
- - meta3:
type: map
description: |
Expand Down Expand Up @@ -122,13 +128,27 @@ output:
pattern: "*.pairs.gz"
ontologies:
- edam: http://edamontology.org/format_3989 # GZIP format
versions_chromap:
- - ${task.process}:
type: string
description: The name of the process
- chromap:
type: string
description: The name of the tool
- chromap --version 2>&1:
type: eval
description: The expression to obtain 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 name of the process
- chromap:
type: string
description: The name of the tool
- chromap --version 2>&1:
type: eval
description: The expression to obtain the version of the tool
authors:
- "@mahesh-panchal"
- "@joseespinosa"
Expand Down
20 changes: 12 additions & 8 deletions modules/nf-core/chromap/chromap/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,8 @@ nextflow_process {
]
input[1] = [
[:],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
]
input[2] = CHROMAP_INDEX.out.index
input[3] = []
Expand All @@ -52,7 +53,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}
}
Expand All @@ -71,7 +72,8 @@ nextflow_process {
]
input[1] = [
[:],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
]
input[2] = CHROMAP_INDEX.out.index
input[3] = []
Expand All @@ -85,7 +87,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}
}
Expand All @@ -108,7 +110,8 @@ nextflow_process {
]
input[1] = [
[:],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
]
input[2] = CHROMAP_INDEX.out.index
input[3] = []
Expand All @@ -126,7 +129,7 @@ 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') }
)
}
)
Expand All @@ -147,7 +150,8 @@ nextflow_process {
]
input[1] = [
[:],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
[]
]
input[2] = CHROMAP_INDEX.out.index
input[3] = []
Expand All @@ -161,7 +165,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}
}
Expand Down
129 changes: 30 additions & 99 deletions modules/nf-core/chromap/chromap/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -2,27 +2,6 @@
"sarscov2 - single_end": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": true
},
"test.bed.gz:md5,b23aa9dae812fe84c308df6e18d850be"
]
],
"1": [

],
"2": [

],
"3": [

],
"4": [
"versions.yml:md5,e3ece11a3651bd28b0ea714f94f09da7"
],
"bam": [

],
Expand All @@ -41,41 +20,24 @@
"tagAlign": [

],
"versions": [
"versions.yml:md5,e3ece11a3651bd28b0ea714f94f09da7"
"versions_chromap": [
[
"CHROMAP_CHROMAP",
"chromap",
"0.2.6-r490"
]
]
}
],
"timestamp": "2026-03-23T20:43:54.016775225",
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-08-05T17:49:22.798324749"
"nf-test": "0.9.4",
"nextflow": "26.02.0"
}
},
"sarscov2 - paired_end ": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
"test.bed.gz:md5,f658c1e94adef751ad08e132aac92712"
]
],
"1": [

],
"2": [

],
"3": [

],
"4": [
"versions.yml:md5,e3ece11a3651bd28b0ea714f94f09da7"
],
"bam": [

],
Expand All @@ -94,59 +56,24 @@
"tagAlign": [

],
"versions": [
"versions.yml:md5,e3ece11a3651bd28b0ea714f94f09da7"
"versions_chromap": [
[
"CHROMAP_CHROMAP",
"chromap",
"0.2.6-r490"
]
]
}
],
"timestamp": "2026-03-23T20:44:03.474089743",
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-08-05T17:49:29.530097947"
"nf-test": "0.9.4",
"nextflow": "26.02.0"
}
},
"sarscov2 - single_end - stub": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": true
},
"test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"1": [
[
{
"id": "test",
"single_end": true
},
"test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"2": [
[
{
"id": "test",
"single_end": true
},
"test.tagAlign.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"3": [
[
{
"id": "test",
"single_end": true
},
"test.pairs.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"4": [
"versions.yml:md5,e3ece11a3651bd28b0ea714f94f09da7"
],
"bam": [
[
{
Expand Down Expand Up @@ -183,15 +110,19 @@
"test.tagAlign.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"versions": [
"versions.yml:md5,e3ece11a3651bd28b0ea714f94f09da7"
"versions_chromap": [
[
"CHROMAP_CHROMAP",
"chromap",
"0.2.6-r490"
]
]
}
],
"timestamp": "2026-03-23T20:44:20.71658166",
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-08-05T17:49:42.086410229"
"nf-test": "0.9.4",
"nextflow": "26.02.0"
}
}
}
3 changes: 0 additions & 3 deletions subworkflows/nf-core/fastq_align_chromap/main.nf
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Expand Up @@ -16,13 +16,11 @@ workflow FASTQ_ALIGN_CHROMAP {
ch_pairs_chr_order // channel (optional): [ pairs_chr_order ]

main:
ch_versions = channel.empty()

//
// Map reads with CHROMAP
//
CHROMAP_CHROMAP(ch_reads, ch_fasta_fai, ch_index, ch_barcodes, ch_whitelist, ch_chr_order, ch_pairs_chr_order)
ch_versions = ch_versions.mix(CHROMAP_CHROMAP.out.versions)

//
// Sort, index BAM file and run samtools stats, flagstat and idxstats
Expand All @@ -35,5 +33,4 @@ workflow FASTQ_ALIGN_CHROMAP {
stats = BAM_SORT_STATS_SAMTOOLS.out.stats // channel: [ val(meta), [ stats ] ]
flagstat = BAM_SORT_STATS_SAMTOOLS.out.flagstat // channel: [ val(meta), [ flagstat ] ]
idxstats = BAM_SORT_STATS_SAMTOOLS.out.idxstats // channel: [ val(meta), [ idxstats ] ]
versions = ch_versions // path: versions.yml
}
4 changes: 0 additions & 4 deletions subworkflows/nf-core/fastq_align_chromap/meta.yml
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Expand Up @@ -93,10 +93,6 @@ output:
type: file
description: File containing samtools idxstats output
pattern: "*.{idxstats}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@JoseEspinosa"
maintainers:
Expand Down
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