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Update smncopynumbercaller, ucsc/wigtobigwig, spring, and tiddit to use topic versions #9977

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Update smncopynumbercaller, ucsc/wigtobigwig, spring, and tiddit to use topic versions #9977

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a209db6
ucsc/wigtobigwig
ramprasadn Feb 11, 2026
37f20f9
update tiddit
ramprasadn Feb 11, 2026
f32fef0
update tiddit7sv tests
ramprasadn Feb 11, 2026
c046a15
spring
ramprasadn Feb 11, 2026
b514cad
update mods
ramprasadn Feb 11, 2026
7055035
Merge branch 'master' of github.com:nf-core/modules into updatemodulesrd
ramprasadn Feb 11, 2026
697c4d1
update snaps
ramprasadn Feb 11, 2026
3c925d8
update snap
ramprasadn Feb 11, 2026
5e2ec06
update spring compress test
ramprasadn Feb 11, 2026
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16 changes: 3 additions & 13 deletions modules/nf-core/smncopynumbercaller/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -13,15 +13,15 @@ process SMNCOPYNUMBERCALLER {
output:
tuple val(meta), path("out/*.tsv"), emit: smncopynumber
tuple val(meta), path("out/*.json"), emit: run_metrics
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('smncopynumbercaller'), val("$VERSION"), topic: versions, emit: versions_smncopynumbercaller
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@mashehu mashehu Feb 11, 2026

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Better to write it in directly instead of the version variable.


when:
task.ext.when == null || task.ext.when

script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def VERSION = "1.1.2" // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
VERSION = "1.1.2" // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
"""
echo $bam | tr ' ' '
' > manifest.txt
Expand All @@ -31,24 +31,14 @@ process SMNCOPYNUMBERCALLER {
--prefix $prefix \\
--outDir "out" \\
--threads $task.cpus

cat <<-END_VERSIONS > versions.yml
"${task.process}":
SMNCopyNumberCaller: $VERSION
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
def VERSION = "1.1.2"
VERSION = "1.1.2"
"""
mkdir out
touch out/${prefix}.tsv
touch out/${prefix}.json

cat <<-END_VERSIONS > versions.yml
"${task.process}":
SMNCopyNumberCaller: $VERSION
END_VERSIONS
"""
}
26 changes: 20 additions & 6 deletions modules/nf-core/smncopynumbercaller/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -58,13 +58,27 @@ output:
pattern: "*.{json}"
ontologies:
- edam: http://edamontology.org/format_3464 # JSON
versions_smncopynumbercaller:
- - ${task.process}:
type: string
description: The name of the process
- smncopynumbercaller:
type: string
description: The name of the tool
- $VERSION:
type: string
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
- smncopynumbercaller:
type: string
description: The name of the tool
- $VERSION:
type: string
description: The expression to obtain the version of the tool
authors:
- "@peterpru"
maintainers:
Expand Down
40 changes: 28 additions & 12 deletions modules/nf-core/smncopynumbercaller/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,11 @@
]
],
"2": [
"versions.yml:md5,084e44557eacbb00c1a24dc71ed022cf"
[
"SMNCOPYNUMBERCALLER",
"smncopynumbercaller",
"1.1.2"
]
],
"run_metrics": [
[
Expand All @@ -37,16 +41,20 @@
"test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,084e44557eacbb00c1a24dc71ed022cf"
"versions_smncopynumbercaller": [
[
"SMNCOPYNUMBERCALLER",
"smncopynumbercaller",
"1.1.2"
]
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.4"
"nf-test": "0.9.3",
"nextflow": "25.10.3"
},
"timestamp": "2024-08-27T12:54:27.295453"
"timestamp": "2026-02-11T21:26:46.783248"
},
"test-smncopynumbercaller": {
"content": [
Expand All @@ -68,7 +76,11 @@
]
],
"2": [
"versions.yml:md5,084e44557eacbb00c1a24dc71ed022cf"
[
"SMNCOPYNUMBERCALLER",
"smncopynumbercaller",
"1.1.2"
]
],
"run_metrics": [
[
Expand All @@ -86,15 +98,19 @@
"test.tsv:md5,0de62f196972c17e1701aa8cea0849f9"
]
],
"versions": [
"versions.yml:md5,084e44557eacbb00c1a24dc71ed022cf"
"versions_smncopynumbercaller": [
[
"SMNCOPYNUMBERCALLER",
"smncopynumbercaller",
"1.1.2"
]
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.4"
"nf-test": "0.9.3",
"nextflow": "25.10.3"
},
"timestamp": "2024-08-27T12:54:21.71312"
"timestamp": "2026-02-11T21:26:43.145754"
}
}
16 changes: 3 additions & 13 deletions modules/nf-core/spring/compress/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -12,15 +12,15 @@ process SPRING_COMPRESS {

output:
tuple val(meta), path("*.spring"), emit: spring
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('spring'), val("$VERSION"), topic: versions, emit: versions_spring

when:
task.ext.when == null || task.ext.when

script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def VERSION = '1.1.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
VERSION = '1.1.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
def input = meta.single_end ? "-i ${fastq1}" : "-i ${fastq1} ${fastq2}"

"""
Expand All @@ -31,23 +31,13 @@ process SPRING_COMPRESS {
$args \\
${input} \\
-o ${prefix}.spring

cat <<-END_VERSIONS > versions.yml
"${task.process}":
spring: ${VERSION}
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
def VERSION = '1.1.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
VERSION = '1.1.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
"""
touch ${prefix}.spring

cat <<-END_VERSIONS > versions.yml
"${task.process}":
spring: ${VERSION}
END_VERSIONS
"""

}
26 changes: 20 additions & 6 deletions modules/nf-core/spring/compress/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -42,13 +42,27 @@ output:
description: One sequence file in spring compressed format.
pattern: "*.{spring}"
ontologies: []
versions_spring:
- - ${task.process}:
type: string
description: The name of the process
- spring:
type: string
description: The name of the tool
- $VERSION:
type: string
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
- spring:
type: string
description: The name of the tool
- $VERSION:
type: string
description: The expression to obtain the version of the tool
authors:
- "@xec-cm"
maintainers:
Expand Down
8 changes: 4 additions & 4 deletions modules/nf-core/spring/compress/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ nextflow_process {
{ assert process.success },
{ assert snapshot(
file(process.out.spring[0][1]).name,
process.out.versions
process.out.findAll {key, value -> key.startsWith("versions")}
).match()
}
)
Expand All @@ -57,7 +57,7 @@ nextflow_process {
{ assert process.success },
{ assert snapshot(
file(process.out.spring[0][1]).name,
process.out.versions
process.out.findAll {key, value -> key.startsWith("versions")}
).match()
}
)
Expand Down Expand Up @@ -86,7 +86,7 @@ nextflow_process {
{ assert process.success },
{ assert snapshot(
file(process.out.spring[0][1]).name,
process.out.versions
process.out.findAll {key, value -> key.startsWith("versions")}
).match()
}
)
Expand Down Expand Up @@ -115,7 +115,7 @@ nextflow_process {
{ assert process.success },
{ assert snapshot(
file(process.out.spring[0][1]).name,
process.out.versions
process.out.findAll {key, value -> key.startsWith("versions")}
).match()
}
)
Expand Down
72 changes: 48 additions & 24 deletions modules/nf-core/spring/compress/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -2,53 +2,77 @@
"test-spring-compress-single-end-stub": {
"content": [
"test.spring",
[
"versions.yml:md5,2882bc3a3593cb048417c38e7452a788"
]
{
"versions_spring": [
[
"SPRING_COMPRESS",
"spring",
"1.1.1"
]
]
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nf-test": "0.9.3",
"nextflow": "25.10.3"
},
"timestamp": "2024-10-08T09:56:05.145653656"
"timestamp": "2026-02-11T21:45:11.688457"
},
"test-spring-compress-paired-end-stub": {
"content": [
"test.spring",
[
"versions.yml:md5,2882bc3a3593cb048417c38e7452a788"
]
{
"versions_spring": [
[
"SPRING_COMPRESS",
"spring",
"1.1.1"
]
]
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nf-test": "0.9.3",
"nextflow": "25.10.3"
},
"timestamp": "2024-10-08T09:56:11.592113469"
"timestamp": "2026-02-11T21:45:15.293977"
},
"test-spring-compress-single-end": {
"content": [
"test.spring",
[
"versions.yml:md5,2882bc3a3593cb048417c38e7452a788"
]
{
"versions_spring": [
[
"SPRING_COMPRESS",
"spring",
"1.1.1"
]
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.4"
"nf-test": "0.9.3",
"nextflow": "25.10.3"
},
"timestamp": "2024-08-27T12:27:30.458355"
"timestamp": "2026-02-11T21:45:04.039231"
},
"test-spring-compress-paired-end": {
"content": [
"test.spring",
[
"versions.yml:md5,2882bc3a3593cb048417c38e7452a788"
]
{
"versions_spring": [
[
"SPRING_COMPRESS",
"spring",
"1.1.1"
]
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.4"
"nf-test": "0.9.3",
"nextflow": "25.10.3"
},
"timestamp": "2024-08-27T12:27:35.271383"
"timestamp": "2026-02-11T21:45:08.295221"
}
}
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