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LouisLeNezet wants to merge 4 commits into from
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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
ec648a0
Merge branch 'master' into chromap
LouisLeNezet Apr 2, 2026
b51a7c2
Merge branch 'master' into chromap
LouisLeNezet Apr 2, 2026
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1 change: 0 additions & 1 deletion modules/nf-core/chromap/chromap/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,6 @@ process CHROMAP_CHROMAP {
tuple val(meta), path("*.tagAlign.gz"), optional:true, emit: tagAlign
tuple val(meta), path("*.pairs.gz") , optional:true, emit: pairs
tuple val("${task.process}"), val('chromap'), eval("chromap --version 2>&1"), topic: versions, emit: versions_chromap
tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'"), topic: versions, emit: versions_samtools

when:
task.ext.when == null || task.ext.when
Expand Down
24 changes: 3 additions & 21 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 @@ -47,7 +48,7 @@ input:
- fai:
type: file
description: |
The fasta reference index file.
The fasta reference file index.
ontologies: []
- - meta3:
type: map
Expand Down Expand Up @@ -137,16 +138,6 @@ output:
- chromap --version 2>&1:
type: eval
description: The expression to obtain the version of the tool
versions_samtools:
- - ${task.process}:
type: string
description: The name of the process
- samtools:
type: string
description: The name of the tool
- samtools version | sed '1!d;s/.* //':
type: eval
description: The expression to obtain the version of the tool
topics:
versions:
- - ${task.process}:
Expand All @@ -158,15 +149,6 @@ topics:
- chromap --version 2>&1:
type: eval
description: The expression to obtain the version of the tool
- - ${task.process}:
type: string
description: The name of the process
- samtools:
type: string
description: The name of the tool
- samtools version | sed '1!d;s/.* //':
type: eval
description: The expression to obtain the version of the tool
authors:
- "@mahesh-panchal"
- "@joseespinosa"
Expand Down
10 changes: 5 additions & 5 deletions modules/nf-core/chromap/chromap/tests/main.nf.test
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Expand Up @@ -54,7 +54,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}
}
Expand Down Expand Up @@ -88,7 +88,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}
}
Expand Down Expand Up @@ -130,7 +130,7 @@ 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 @@ -152,7 +152,7 @@ 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.fai', checkIfExists: true)
[]
]
input[2] = CHROMAP_INDEX.out.index
input[3] = []
Expand All @@ -166,7 +166,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}
}
Expand Down
232 changes: 11 additions & 221 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 @@ -2,38 +2,6 @@
"sarscov2 - single_end": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": true
},
"test.bed.gz:md5,b23aa9dae812fe84c308df6e18d850be"
]
],
"1": [

],
"2": [

],
"3": [

],
"4": [
[
"CHROMAP_CHROMAP",
"chromap",
"0.3.2-r518"
]
],
"5": [
[
"CHROMAP_CHROMAP",
"samtools",
"1.23.1"
]
],
"bam": [

],
Expand All @@ -56,59 +24,20 @@
[
"CHROMAP_CHROMAP",
"chromap",
"0.3.2-r518"
]
],
"versions_samtools": [
[
"CHROMAP_CHROMAP",
"samtools",
"1.23.1"
"0.2.6-r490"
]
]
}
],
"timestamp": "2026-03-27T17:32:15.943898",
"timestamp": "2026-03-23T20:43:54.016775225",
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.4"
"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": [
[
"CHROMAP_CHROMAP",
"chromap",
"0.3.2-r518"
]
],
"5": [
[
"CHROMAP_CHROMAP",
"samtools",
"1.23.1"
]
],
"bam": [

],
Expand All @@ -131,77 +60,20 @@
[
"CHROMAP_CHROMAP",
"chromap",
"0.3.2-r518"
]
],
"versions_samtools": [
[
"CHROMAP_CHROMAP",
"samtools",
"1.23.1"
"0.2.6-r490"
]
]
}
],
"timestamp": "2026-03-27T17:32:51.441586",
"timestamp": "2026-03-23T20:44:03.474089743",
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.4"
"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": [
[
"CHROMAP_CHROMAP",
"chromap",
"0.3.2-r518"
]
],
"5": [
[
"CHROMAP_CHROMAP",
"samtools",
"1.23.1"
]
],
"bam": [
[
{
Expand Down Expand Up @@ -242,97 +114,15 @@
[
"CHROMAP_CHROMAP",
"chromap",
"0.3.2-r518"
]
],
"versions_samtools": [
[
"CHROMAP_CHROMAP",
"samtools",
"1.23.1"
]
]
}
],
"timestamp": "2026-03-27T17:33:28.468564",
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.4"
}
},
"sarscov2 - paired_end": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
"test.bed.gz:md5,f658c1e94adef751ad08e132aac92712"
]
],
"1": [

],
"2": [

],
"3": [

],
"4": [
[
"CHROMAP_CHROMAP",
"chromap",
"0.3.2-r518"
]
],
"5": [
[
"CHROMAP_CHROMAP",
"samtools",
"1.23.1"
]
],
"bam": [

],
"bed": [
[
{
"id": "test",
"single_end": false
},
"test.bed.gz:md5,f658c1e94adef751ad08e132aac92712"
]
],
"pairs": [

],
"tagAlign": [

],
"versions_chromap": [
[
"CHROMAP_CHROMAP",
"chromap",
"0.3.2-r518"
]
],
"versions_samtools": [
[
"CHROMAP_CHROMAP",
"samtools",
"1.23.1"
"0.2.6-r490"
]
]
}
],
"timestamp": "2026-04-01T22:26:29.768814",
"timestamp": "2026-03-23T20:44:20.71658166",
"meta": {
"nf-test": "0.9.4",
"nextflow": "25.10.4"
"nextflow": "26.02.0"
}
}
}
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