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Merged
SPPearce merged 3 commits into from
Jul 20, 2026
+89 −78
Merged

migrate sequencetools/pileupcaller to version topic #12381

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7a444cb
migrate to version topic
TCLamnidis Jul 17, 2026
88e6495
Update nf-test and snapshots
TCLamnidis Jul 20, 2026
063ab74
update test and snapshot. Thanks @mashehu
TCLamnidis Jul 20, 2026
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12 changes: 1 addition & 11 deletions modules/nf-core/sequencetools/pileupcaller/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ process SEQUENCETOOLS_PILEUPCALLER {
tuple val(meta), path("*.geno"), path("*.snp"), path("*.ind"), emit: eigenstrat, optional:true
tuple val(meta), path("*.bed") , path("*.bim"), path("*.fam"), emit: plink , optional:true
tuple val(meta), path("*.freqsum.gz") , emit: freqsum , optional:true
path "versions.yml" , emit: versions
tuple val("${task.process}"), val("sequencetools"), eval("pileupCaller --version 2>&1"), topic: versions, emit: versions_pileupcaller

when:
task.ext.when == null || task.ext.when
Expand All @@ -36,11 +36,6 @@ process SEQUENCETOOLS_PILEUPCALLER {
${sample_names} \\
${args} \\
${freqsum_output}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
sequencetools: \$(echo \$(pileupCaller --version 2>&1) )
END_VERSIONS
"""

stub:
Expand All @@ -55,10 +50,5 @@ process SEQUENCETOOLS_PILEUPCALLER {
${freqsum_output}
${plink_output}
${eigenstrat_output}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
sequencetools: \$(echo \$(pileupCaller --version 2>&1) )
END_VERSIONS
"""
}
61 changes: 37 additions & 24 deletions modules/nf-core/sequencetools/pileupcaller/meta.yml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
name: "sequencetools_pileupcaller"
description: PileupCaller is a tool to create genotype calls from bam files using
read-sampling methods
description: PileupCaller is a tool to create genotype calls from bam files
using read-sampling methods
keywords:
- genotyping
- mpileup
Expand All @@ -17,10 +17,10 @@ tools:
homepage: "https://github.com/stschiff/sequenceTools"
documentation: "https://github.com/stschiff/sequenceTools#readme"
tool_dev_url: "https://github.com/stschiff/sequenceTools"
licence: ["MIT"]
licence:
- "MIT"
identifier: ""
input:
# Only when we have meta
- - meta:
type: map
description: |
Expand All @@ -41,7 +41,6 @@ input:
description: File containing the sample names
ontologies: []
output:
#Only when we have meta
eigenstrat:
- - meta:
type: map
Expand All @@ -50,20 +49,20 @@ output:
e.g. [ id:'test', single_end:false ]
- "*.geno":
type: file
description: A tuple containing the output Eigenstrat-formatted geno, snp
and ind files.
description: A tuple containing the output Eigenstrat-formatted geno,
snp and ind files.
pattern: "*.{geno,snp,ind}.txt"
ontologies: []
- "*.snp":
type: file
description: A tuple containing the output Eigenstrat-formatted geno, snp
and ind files.
description: A tuple containing the output Eigenstrat-formatted geno,
snp and ind files.
pattern: "*.{geno,snp,ind}.txt"
ontologies: []
- "*.ind":
type: file
description: A tuple containing the output Eigenstrat-formatted geno, snp
and ind files.
description: A tuple containing the output Eigenstrat-formatted geno,
snp and ind files.
pattern: "*.{geno,snp,ind}.txt"
ontologies: []
plink:
Expand All @@ -74,20 +73,20 @@ output:
e.g. [ id:'test', single_end:false ]
- "*.bed":
type: file
description: A tuple containing the output Plink-formatted bed, bim and fam
files.
description: A tuple containing the output Plink-formatted bed, bim and
fam files.
pattern: "*.{bed,bim,fam}"
ontologies: []
- "*.bim":
type: file
description: A tuple containing the output Plink-formatted bed, bim and fam
files.
description: A tuple containing the output Plink-formatted bed, bim and
fam files.
pattern: "*.{bed,bim,fam}"
ontologies: []
- "*.fam":
type: file
description: A tuple containing the output Plink-formatted bed, bim and fam
files.
description: A tuple containing the output Plink-formatted bed, bim and
fam files.
pattern: "*.{bed,bim,fam}"
ontologies: []
freqsum:
Expand All @@ -101,14 +100,28 @@ output:
description: The output freqsum-formatted file.
pattern: "*.freqsum.gz"
ontologies:
- edam: http://edamontology.org/format_3989 # GZIP format
- edam: http://edamontology.org/format_3989
versions_pileupcaller:
- - ${task.process}:
type: string
description: The name of the process
- sequencetools:
type: string
description: The name of the tool
- pileupCaller --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
- sequencetools:
type: string
description: The name of the tool
- pileupCaller --version 2>&1:
type: eval
description: The expression to obtain the version of the tool
authors:
- "@TCLamnidis"
maintainers:
Expand Down
9 changes: 3 additions & 6 deletions modules/nf-core/sequencetools/pileupcaller/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -30,8 +30,7 @@ nextflow_process {
assertAll(
{ assert snapshot(
path(process.out.freqsum[0][1]).linesGzip[0..4],
process.out.versions,
path(process.out.versions[0]).yaml
process.out.findAll { key, val -> key.startsWith('versions') },
).match() }
)
}
Expand Down Expand Up @@ -59,8 +58,7 @@ nextflow_process {
file(process.out.eigenstrat[0][1]).name,
process.out.eigenstrat[0][2],
process.out.eigenstrat[0][3],
process.out.versions,
path(process.out.versions[0]).yaml
process.out.findAll { key, val -> key.startsWith('versions') },
).match() }
)
}
Expand Down Expand Up @@ -88,8 +86,7 @@ nextflow_process {
file(process.out.plink[0][1]).name,
process.out.plink[0][2],
process.out.plink[0][3],
process.out.versions,
path(process.out.versions[0]).yaml
process.out.findAll { key, val -> key.startsWith('versions') },
).match() }
)
}
Expand Down
85 changes: 48 additions & 37 deletions modules/nf-core/sequencetools/pileupcaller/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -4,20 +4,21 @@
"test.geno",
"test.snp:md5,1c64da4b67bbc46ea4ac3146efb37346",
"test.ind:md5,f8d5d94b39e3693452af54688649aaad",
[
"versions.yml:md5,2ce04439173fcba8671d312e79f3a148"
],
{
"SEQUENCETOOLS_PILEUPCALLER": {
"sequencetools": "1.6.0.0"
}
"versions_pileupcaller": [
[
"SEQUENCETOOLS_PILEUPCALLER",
"sequencetools",
"1.6.0.0"
]
]
}
],
"timestamp": "2026-07-20T15:43:48.322784",
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
},
"timestamp": "2025-04-23T10:48:45.195842"
"nf-test": "0.9.5",
"nextflow": "26.04.4"
}
},
"freqsum - stub": {
"content": [
Expand All @@ -37,7 +38,11 @@
]
],
"3": [
"versions.yml:md5,2ce04439173fcba8671d312e79f3a148"
[
"SEQUENCETOOLS_PILEUPCALLER",
"sequencetools",
"1.6.0.0"
]
],
"eigenstrat": [

Expand All @@ -53,36 +58,41 @@
"plink": [

],
"versions": [
"versions.yml:md5,2ce04439173fcba8671d312e79f3a148"
"versions_pileupcaller": [
[
"SEQUENCETOOLS_PILEUPCALLER",
"sequencetools",
"1.6.0.0"
]
]
}
],
"timestamp": "2026-07-20T15:44:21.402431",
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
},
"timestamp": "2025-04-23T09:23:25.707102"
"nf-test": "0.9.5",
"nextflow": "26.04.4"
}
},
"plink": {
"content": [
"test.bed",
"test.bim:md5,4618dec3be68386e18562a3f4812e0dc",
"test.fam:md5,f3e98d680273a975b00ea6e0d67cfad1",
[
"versions.yml:md5,2ce04439173fcba8671d312e79f3a148"
],
{
"SEQUENCETOOLS_PILEUPCALLER": {
"sequencetools": "1.6.0.0"
}
"versions_pileupcaller": [
[
"SEQUENCETOOLS_PILEUPCALLER",
"sequencetools",
"1.6.0.0"
]
]
}
],
"timestamp": "2026-07-20T15:44:13.398562",
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
},
"timestamp": "2025-04-23T10:49:59.522249"
"nf-test": "0.9.5",
"nextflow": "26.04.4"
}
},
"freqsum": {
"content": [
Expand All @@ -93,19 +103,20 @@
"21\t11002011\tT\tC\t-1",
"21\t14601415\tG\tA\t-1"
],
[
"versions.yml:md5,2ce04439173fcba8671d312e79f3a148"
],
{
"SEQUENCETOOLS_PILEUPCALLER": {
"sequencetools": "1.6.0.0"
}
"versions_pileupcaller": [
[
"SEQUENCETOOLS_PILEUPCALLER",
"sequencetools",
"1.6.0.0"
]
]
}
],
"timestamp": "2026-07-20T15:43:22.87245",
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
},
"timestamp": "2025-04-23T21:11:12.666134"
"nf-test": "0.9.5",
"nextflow": "26.04.4"
}
}
}