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gamma gamma update2topics #11462

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b8f4e5f
Adds stub block to gamma_gamma
mribeirodantas May 1, 2026
5759411
Update gamma/gamma to using the versions topic channel
mribeirodantas May 1, 2026
ad9c087
Merge branch 'master' into gamma_gamma_update2topics
mribeirodantas May 2, 2026
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25 changes: 15 additions & 10 deletions modules/nf-core/gamma/gamma/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -14,19 +14,19 @@ process GAMMA_GAMMA {
path(db)

output:
tuple val(meta), path("*.gamma") , emit: gamma
tuple val(meta), path("*.psl") , emit: psl
tuple val(meta), path("*.gff") , optional:true , emit: gff
tuple val(meta), path("*.fasta"), optional:true , emit: fasta
path "versions.yml" , emit: versions
tuple val(meta), path("*.gamma") , emit: gamma
tuple val(meta), path("*.psl") , emit: psl
tuple val(meta), path("*.gff") , optional:true , emit: gff
tuple val(meta), path("*.fasta"), optional:true , emit: fasta
// WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
tuple val("${task.process}"), val('gamma'), val("2.1"), emit: versions_gamma, topic: versions

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

script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def VERSION = '2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
"""
if [[ ${fasta} == *.gz ]]
then
Expand All @@ -44,9 +44,14 @@ process GAMMA_GAMMA {
$db \\
$prefix
fi
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gamma: $VERSION
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.gamma
touch ${prefix}.psl
touch ${prefix}.gff
touch ${prefix}.fasta
"""
}
26 changes: 20 additions & 6 deletions modules/nf-core/gamma/gamma/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -75,13 +75,27 @@ output:
description: multifasta file of the gene matches
pattern: "*.{fasta}"
ontologies: []
versions_gamma:
- - ${task.process}:
type: string
description: The name of the process
- gamma:
type: string
description: The name of the tool
- "2.1":
type: string
description: The hard-coded 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
- gamma:
type: string
description: The name of the tool
- "2.1":
type: string
description: The hard-coded version of the tool
authors:
- "@sateeshperi"
- "@rastanton"
Expand Down
44 changes: 30 additions & 14 deletions modules/nf-core/gamma/gamma/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,11 @@
]
],
"4": [
"versions.yml:md5,cb429c7c459f700b16278ee01b8c46c7"
[
"GAMMA_GAMMA",
"gamma",
"2.1"
]
],
"fasta": [
[
Expand Down Expand Up @@ -65,16 +69,20 @@
"test.psl:md5,f489ce4602ddbcb692d5781ee3fbf449"
]
],
"versions": [
"versions.yml:md5,cb429c7c459f700b16278ee01b8c46c7"
"versions_gamma": [
[
"GAMMA_GAMMA",
"gamma",
"2.1"
]
]
}
],
"timestamp": "2026-05-01T12:25:09.793968",
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.4"
},
"timestamp": "2024-08-28T13:46:17.70616"
"nf-test": "0.9.4",
"nextflow": "26.04.0"
}
},
"test-gamma": {
"content": [
Expand Down Expand Up @@ -110,7 +118,11 @@
]
],
"4": [
"versions.yml:md5,cb429c7c459f700b16278ee01b8c46c7"
[
"GAMMA_GAMMA",
"gamma",
"2.1"
]
],
"fasta": [
[
Expand Down Expand Up @@ -142,15 +154,19 @@
"test.psl:md5,162a2757ed3b167ae1e0cdb24213f940"
]
],
"versions": [
"versions.yml:md5,cb429c7c459f700b16278ee01b8c46c7"
"versions_gamma": [
[
"GAMMA_GAMMA",
"gamma",
"2.1"
]
]
}
],
"timestamp": "2026-05-01T12:25:13.827116",
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.4"
},
"timestamp": "2024-08-28T13:46:24.433086"
"nf-test": "0.9.4",
"nextflow": "26.04.0"
}
}
}
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