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Swap poolsnp to topics #12282

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7613d3f
Swap poolsnp to topics
SPPearce Jul 8, 2026
9d182d6
Update tests
SPPearce Jul 8, 2026
d69a6bf
max_cov not stable on conda
SPPearce Jul 10, 2026
dab14da
Merge branch 'master' into poolsnp_topics
SPPearce Jul 10, 2026
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14 changes: 1 addition & 13 deletions modules/nf-core/poolsnp/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -16,15 +16,14 @@ process POOLSNP {
tuple val(meta), path("*.vcf.gz") , emit: vcf
tuple val(meta), path("*cov-*.txt"), emit: max_cov , optional: true
tuple val(meta), path("*BS.txt.gz"), emit: bad_sites, optional: true
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('poolsnp'), val('1.0.1'), emit: versions_poolsnp, topic: versions // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.

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

script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def VERSION = '1.0.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
assert (!max_cov && max_cov_file) || (max_cov && !max_cov_file)

"""
Expand All @@ -36,27 +35,16 @@ process POOLSNP {
jobs=${task.cpus} \\
max-cov=${max_cov ? "${max_cov}" : "\$PWD/${max_cov_file}"} \\
$args

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

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
def VERSION = '1.0.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.

"""
echo "##fileformat=VCFv4.2" > ${prefix}.vcf
echo "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO" >> ${prefix}.vcf
gzip ${prefix}.vcf
${max_cov ? "touch ${prefix}_cov-${max_cov}.txt" : ""}
echo "" | gzip > ${prefix}_BS.txt.gz

cat <<-END_VERSIONS > versions.yml
${task.process}:
poolsnp: "${VERSION}"
END_VERSIONS
"""
}
48 changes: 32 additions & 16 deletions modules/nf-core/poolsnp/meta.yml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
name: "poolsnp"
description: PoolSNP is a heuristic SNP caller, which uses an MPILEUP file and a reference
genome in FASTA format as inputs.
description: PoolSNP is a heuristic SNP caller, which uses an MPILEUP file and a
reference genome in FASTA format as inputs.
keywords:
- poolseq
- mpileup
Expand All @@ -12,7 +11,8 @@ tools:
a reference genome in FASTA format as inputs."
homepage: "https://github.com/capoony/PoolSNP"
documentation: "https://github.com/capoony/PoolSNP/blob/master/README.md"
licence: ["Apache-2.0"]
licence:
- "Apache-2.0"
args_id: "$args"

identifier: ""
Expand Down Expand Up @@ -77,8 +77,8 @@ output:
e.g. `[ id:'sample1', single_end:false ]`
- "*.vcf.gz":
type: file
description: Gzipped VCF file containing allele counts and frequencies for
every position and library
description: Gzipped VCF file containing allele counts and frequencies
for every position and library
pattern: "*.vcf.gz"
ontologies:
- edam: http://edamontology.org/format_3989 # GZIP format
Expand All @@ -90,8 +90,8 @@ output:
e.g. `[ id:'sample1', single_end:false ]`
- "*cov-*.txt":
type: file
description: File containing the maximum coverage thresholds for all chromosomal
arms and libraries
description: File containing the maximum coverage thresholds for all
chromosomal arms and libraries
pattern: "*cov-*.txt"
ontologies: []
bad_sites:
Expand All @@ -102,19 +102,35 @@ output:
e.g. `[ id:'sample1', single_end:false ]`
- "*BS.txt.gz":
type: file
description: File containing a list of sites (variable and invariable) that
did not pass the SNP calling criteria
description: File containing a list of sites (variable and invariable)
that did not pass the SNP calling criteria
pattern: "*BS.txt.gz"
optional: true
ontologies:
- edam: http://edamontology.org/format_3989 # GZIP format
versions_poolsnp:
- - ${task.process}:
type: string
description: The name of the process
- poolsnp:
type: string
description: The name of the tool
- 1.0.1:
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
- poolsnp:
type: string
description: The name of the tool
- 1.0.1:
type: string
description: The expression to obtain the version of the tool

authors:
- "@abhilesh"
maintainers:
Expand Down
21 changes: 8 additions & 13 deletions modules/nf-core/poolsnp/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -51,12 +51,11 @@ nextflow_process {
}

then {
assert process.success
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.versions,
path(process.out.vcf[0][1]).vcf.variantsMD5,
process.out.max_cov
sanitizeOutput(process.out, unstableKeys: ['max_cov', 'vcf'])
).match()
}
)
Expand All @@ -82,11 +81,11 @@ nextflow_process {
}

then {
assert process.success
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.versions,
path(process.out.vcf[0][1]).vcf.variantsMD5
path(process.out.vcf[0][1]).vcf.variantsMD5,
sanitizeOutput(process.out, unstableKeys: ['max_cov', 'vcf'])
).match()
}
)
Expand Down Expand Up @@ -118,7 +117,7 @@ nextflow_process {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.versions,
process.out.findAll { key, val -> key.startsWith("versions")},
path(process.out.vcf[0][1]).vcf.variantsMD5,
process.out.max_cov
).match()
Expand Down Expand Up @@ -148,13 +147,9 @@ nextflow_process {
}

then {
assert process.success
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.versions,
path(process.out.vcf[0][1]).vcf.variantsMD5
).match()
}
{ assert snapshot(sanitizeOutput(process.out)).match()}
)
}
}
Expand Down
151 changes: 114 additions & 37 deletions modules/nf-core/poolsnp/tests/main.nf.test.snap
View file
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Original file line number Diff line number Diff line change
@@ -1,9 +1,15 @@
{
"sarscov2 - mpileup - max_cov - stub": {
"content": [
[
"versions.yml:md5,2bc174a10a560499c04e6b35ce86fed0"
],
{
"versions_poolsnp": [
[
"POOLSNP",
"poolsnp",
"1.0.1"
]
]
},
"d41d8cd98f00b204e9800998ecf8427e",
[
[
Expand All @@ -14,57 +20,128 @@
]
]
],
"timestamp": "2026-07-08T05:32:01.870716039",
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.6"
},
"timestamp": "2025-05-12T17:14:40.699184098"
"nf-test": "0.9.5",
"nextflow": "26.04.0"
}
},
"sarscov2 - mpileup - max_cov_file - stub": {
"content": [
[
"versions.yml:md5,2bc174a10a560499c04e6b35ce86fed0"
],
"d41d8cd98f00b204e9800998ecf8427e"
{
"bad_sites": [
[
{
"id": "test"
},
"test_BS.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"max_cov": [

],
"vcf": [
[
{
"id": "test"
},
"test.vcf.gz:md5,4a36fe59dc6865cd5ee9e7ecd936106e"
]
],
"versions_poolsnp": [
[
"POOLSNP",
"poolsnp",
"1.0.1"
]
]
}
],
"timestamp": "2026-07-10T05:55:27.287972382",
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.4"
},
"timestamp": "2024-08-16T15:56:12.188459"
"nf-test": "0.9.5",
"nextflow": "26.04.0"
}
},
"sarscov2 - mpileup - max_cov": {
"content": [
[
"versions.yml:md5,2bc174a10a560499c04e6b35ce86fed0"
],
"46e2d27f13d700dbdb061091308f1555",
[
[
{
"id": "test"
},
"test-cov-0.7.txt:md5,ccbb119522c09daa976a9015ba999329"
{
"bad_sites": [
[
{
"id": "test"
},
"test_BS.txt.gz:md5,41251fba6925d7428836739822168bd1"
]
],
"max_cov": [
[
{
"id": "test"
},
"test-cov-0.7.txt"
]
],
"vcf": [
[
{
"id": "test"
},
"test.vcf.gz"
]
],
"versions_poolsnp": [
[
"POOLSNP",
"poolsnp",
"1.0.1"
]
]
]
}
],
"timestamp": "2026-07-10T05:55:07.885346374",
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.6"
},
"timestamp": "2025-05-12T17:14:11.680742"
"nf-test": "0.9.5",
"nextflow": "26.04.0"
}
},
"sarscov2 - mpileup - max_cov_file": {
"content": [
[
"versions.yml:md5,2bc174a10a560499c04e6b35ce86fed0"
],
"46e2d27f13d700dbdb061091308f1555"
"46e2d27f13d700dbdb061091308f1555",
{
"bad_sites": [
[
{
"id": "test"
},
"test_BS.txt.gz:md5,41251fba6925d7428836739822168bd1"
]
],
"max_cov": [

],
"vcf": [
[
{
"id": "test"
},
"test.vcf.gz"
]
],
"versions_poolsnp": [
[
"POOLSNP",
"poolsnp",
"1.0.1"
]
]
}
],
"timestamp": "2026-07-10T05:55:14.671243804",
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.4"
},
"timestamp": "2024-08-16T15:31:24.140061"
"nf-test": "0.9.5",
"nextflow": "26.04.0"
}
}
}
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