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Merged
merged 10 commits into from
Apr 9, 2025
Merged

nf-test migration: plink/indeppairwise #8133

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0182e4f
Migrated pytest to nf-test for `plink/indeppairwise` module & added s…
mantisps Mar 26, 2025
f390711
Merge remote-tracking branch 'upstream/master' into plink/indeppairwi…
mantisps Mar 26, 2025
4285c34
Update modules/nf-core/plink/indeppairwise/tests/main.nf.test
mantisps Mar 26, 2025
aa56d08
Merge branch 'master' into plink/indeppairwise_nftest
mantisps Mar 26, 2025
b4a7a6d
Merge branch 'master' into plink/indeppairwise_nftest
maxulysse Mar 27, 2025
ffb0312
Fixed nf-test based on PR comments.
mantisps Mar 28, 2025
3dd4455
Restored `.pre-commit-config.yaml` to original state.
mantisps Mar 28, 2025
a71e8ce
Merge branch 'master' into plink/indeppairwise_nftest
mantisps Mar 28, 2025
931ae12
Update modules/nf-core/plink/indeppairwise/main.nf
mantisps Mar 31, 2025
d0961d9
Merge branch 'master' into plink/indeppairwise_nftest
mantisps Mar 31, 2025
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21 changes: 17 additions & 4 deletions modules/nf-core/plink/indeppairwise/main.nf
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Original file line number Diff line number Diff line change
@@ -1,4 +1,3 @@

process PLINK_INDEPPAIRWISE {
tag "$meta.id"
label 'process_low'
Expand Down Expand Up @@ -31,10 +30,24 @@ process PLINK_INDEPPAIRWISE {
--bed ${bed} \\
--bim ${bim} \\
--fam ${fam} \\
--threads $task.cpus \\
--threads ${task.cpus} \\
--indep-pairwise ${window_size} ${variant_count} ${r2_threshold} \\
$args \\
--out $prefix
${args} \\
--out ${prefix}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
plink: \$(echo \$(plink --version) | sed 's/^PLINK v//;s/64.*//')
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"

"""
touch ${prefix}.prune.in
touch ${prefix}.prune.out

cat <<-END_VERSIONS > versions.yml
"${task.process}":
plink: \$(echo \$(plink --version) | sed 's/^PLINK v//;s/64.*//')
Expand Down
76 changes: 76 additions & 0 deletions modules/nf-core/plink/indeppairwise/tests/main.nf.test
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@@ -0,0 +1,76 @@
nextflow_process {

name "Test Process PLINK_INDEPPAIRWISE"
script "../main.nf"
process "PLINK_INDEPPAIRWISE"

tag "modules"
tag "modules_nfcore"
tag "plink"
tag "plink/indeppairwise"
tag "plink/vcf"

setup {

config "./nextflow.config"

params {
module_args = '--make-bed --biallelic-only strict --vcf-half-call haploid --allow-extra-chr'
}

run("PLINK_VCF") {

script "../../vcf/main.nf"

process {
"""
input[0] = [
[id:'test',single_end:false],// meta map
file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz", checkIfExists:true)
]
"""
}
}
}

test("test_plink_indeppairwise") {
when {
process {
"""
input[0] = PLINK_VCF.out.bed.join(PLINK_VCF.out.bim).join(PLINK_VCF.out.fam)
input[1] = Channel.value(50)
input[2] = Channel.value(5)
input[3] = Channel.value(0.2)
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
}

test("test_plink_indeppairwise - stub") {

options "-stub"

when {
process {
"""
input[0] = PLINK_VCF.out.bed.join(PLINK_VCF.out.bim).join(PLINK_VCF.out.fam)
input[1] = Channel.value(50)
input[2] = Channel.value(5)
input[3] = Channel.value(0.2)
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
}
}
108 changes: 108 additions & 0 deletions modules/nf-core/plink/indeppairwise/tests/main.nf.test.snap
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@@ -0,0 +1,108 @@
{
"test_plink_indeppairwise": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
"test.prune.in:md5,dce7ba75405107468f2ce18fc95a9786"
]
],
"1": [
[
{
"id": "test",
"single_end": false
},
"test.prune.out:md5,1f65f71308f2c4a03b9a4a98bbfb11e9"
]
],
"2": [
"versions.yml:md5,dd52fb8375a5ba36e766f25e9028d128"
],
"prunein": [
[
{
"id": "test",
"single_end": false
},
"test.prune.in:md5,dce7ba75405107468f2ce18fc95a9786"
]
],
"pruneout": [
[
{
"id": "test",
"single_end": false
},
"test.prune.out:md5,1f65f71308f2c4a03b9a4a98bbfb11e9"
]
],
"versions": [
"versions.yml:md5,dd52fb8375a5ba36e766f25e9028d128"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
},
"timestamp": "2025-03-26T14:55:08.717872783"
},
"test_plink_indeppairwise - stub": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
"test.prune.in:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
[
{
"id": "test",
"single_end": false
},
"test.prune.out:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"2": [
"versions.yml:md5,dd52fb8375a5ba36e766f25e9028d128"
],
"prunein": [
[
{
"id": "test",
"single_end": false
},
"test.prune.in:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"pruneout": [
[
{
"id": "test",
"single_end": false
},
"test.prune.out:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,dd52fb8375a5ba36e766f25e9028d128"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
},
"timestamp": "2025-03-28T17:45:50.995416015"
}
}
5 changes: 5 additions & 0 deletions modules/nf-core/plink/indeppairwise/tests/nextflow.config
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@@ -0,0 +1,5 @@
process {
withName: "PLINK_VCF" {
ext.args = params.module_args
}
}
3 changes: 0 additions & 3 deletions tests/config/pytest_modules.yml
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Expand Up @@ -154,9 +154,6 @@ paragraph/multigrmpy:
phyloflash:
- modules/nf-core/phyloflash/**
- tests/modules/nf-core/phyloflash/**
plink/indeppairwise:
- modules/nf-core/plink/indeppairwise/**
- tests/modules/nf-core/plink/indeppairwise/**
pneumocat:
- modules/nf-core/pneumocat/**
- tests/modules/nf-core/pneumocat/**
Expand Down
28 changes: 0 additions & 28 deletions tests/modules/nf-core/plink/indeppairwise/main.nf
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8 changes: 0 additions & 8 deletions tests/modules/nf-core/plink/indeppairwise/nextflow.config
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17 changes: 0 additions & 17 deletions tests/modules/nf-core/plink/indeppairwise/test.yml
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