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nf-test migration: plink/indeppairwise (#8133)
* Migrated pytest to nf-test for `plink/indeppairwise` module & added stub run and test to it. * Update modules/nf-core/plink/indeppairwise/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Fixed nf-test based on PR comments. * Restored `.pre-commit-config.yaml` to original state. * Update modules/nf-core/plink/indeppairwise/main.nf Co-authored-by: Simon Pearce <[email protected]> --------- Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Maxime U Garcia <[email protected]>
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‎modules/nf-core/plink/indeppairwise/main.nf

Lines changed: 17 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,3 @@
1-
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process PLINK_INDEPPAIRWISE {
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tag "$meta.id"
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label 'process_low'
@@ -31,10 +30,24 @@ process PLINK_INDEPPAIRWISE {
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--bed ${bed} \\
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--bim ${bim} \\
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--fam ${fam} \\
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--threads $task.cpus \\
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--threads ${task.cpus} \\
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--indep-pairwise ${window_size} ${variant_count} ${r2_threshold} \\
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$args \\
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--out $prefix
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${args} \\
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--out ${prefix}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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plink: \$(echo \$(plink --version) | sed 's/^PLINK v//;s/64.*//')
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END_VERSIONS
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}.prune.in
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touch ${prefix}.prune.out
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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plink: \$(echo \$(plink --version) | sed 's/^PLINK v//;s/64.*//')

‎modules/nf-core/plink/indeppairwise/tests/main.nf.test

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nextflow_process {
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name "Test Process PLINK_INDEPPAIRWISE"
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script "../main.nf"
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process "PLINK_INDEPPAIRWISE"
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tag "modules"
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tag "modules_nfcore"
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tag "plink"
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tag "plink/indeppairwise"
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tag "plink/vcf"
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setup {
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config "./nextflow.config"
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params {
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module_args = '--make-bed --biallelic-only strict --vcf-half-call haploid --allow-extra-chr'
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}
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run("PLINK_VCF") {
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script "../../vcf/main.nf"
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process {
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"""
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input[0] = [
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[id:'test',single_end:false],// meta map
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file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz", checkIfExists:true)
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]
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"""
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}
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}
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}
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test("test_plink_indeppairwise") {
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when {
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process {
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"""
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input[0] = PLINK_VCF.out.bed.join(PLINK_VCF.out.bim).join(PLINK_VCF.out.fam)
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input[1] = Channel.value(50)
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input[2] = Channel.value(5)
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input[3] = Channel.value(0.2)
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(process.out).match() }
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)
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}
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}
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test("test_plink_indeppairwise - stub") {
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options "-stub"
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when {
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process {
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"""
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input[0] = PLINK_VCF.out.bed.join(PLINK_VCF.out.bim).join(PLINK_VCF.out.fam)
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input[1] = Channel.value(50)
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input[2] = Channel.value(5)
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input[3] = Channel.value(0.2)
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(process.out).match() }
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)
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}
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}
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}

‎modules/nf-core/plink/indeppairwise/tests/main.nf.test.snap

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{
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"test_plink_indeppairwise": {
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"content": [
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{
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"0": [
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[
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{
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"id": "test",
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"single_end": false
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},
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"test.prune.in:md5,dce7ba75405107468f2ce18fc95a9786"
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]
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],
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"1": [
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[
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{
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"id": "test",
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"single_end": false
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},
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"test.prune.out:md5,1f65f71308f2c4a03b9a4a98bbfb11e9"
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]
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],
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"2": [
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"versions.yml:md5,dd52fb8375a5ba36e766f25e9028d128"
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],
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"prunein": [
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[
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{
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"id": "test",
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"single_end": false
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},
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"test.prune.in:md5,dce7ba75405107468f2ce18fc95a9786"
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]
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],
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"pruneout": [
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[
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{
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"id": "test",
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"single_end": false
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},
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"test.prune.out:md5,1f65f71308f2c4a03b9a4a98bbfb11e9"
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]
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],
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"versions": [
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"versions.yml:md5,dd52fb8375a5ba36e766f25e9028d128"
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]
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}
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "24.10.5"
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},
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"timestamp": "2025-03-26T14:55:08.717872783"
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},
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"test_plink_indeppairwise - stub": {
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"content": [
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{
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"0": [
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[
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{
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"id": "test",
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"single_end": false
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},
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"test.prune.in:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"1": [
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[
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{
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"id": "test",
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"single_end": false
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},
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"test.prune.out:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"2": [
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"versions.yml:md5,dd52fb8375a5ba36e766f25e9028d128"
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],
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"prunein": [
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[
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{
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"id": "test",
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"single_end": false
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},
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"test.prune.in:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"pruneout": [
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[
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{
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"id": "test",
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"single_end": false
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},
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"test.prune.out:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"versions": [
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"versions.yml:md5,dd52fb8375a5ba36e766f25e9028d128"
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]
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}
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "24.10.5"
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},
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"timestamp": "2025-03-28T17:45:50.995416015"
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}
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}

‎modules/nf-core/plink/indeppairwise/tests/nextflow.config

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process {
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withName: "PLINK_VCF" {
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ext.args = params.module_args
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}
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}

‎tests/config/pytest_modules.yml

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Original file line numberDiff line numberDiff line change
@@ -149,9 +149,6 @@ paragraph/multigrmpy:
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phyloflash:
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- modules/nf-core/phyloflash/**
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- tests/modules/nf-core/phyloflash/**
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plink/indeppairwise:
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- modules/nf-core/plink/indeppairwise/**
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- tests/modules/nf-core/plink/indeppairwise/**
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pneumocat:
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- modules/nf-core/pneumocat/**
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- tests/modules/nf-core/pneumocat/**

‎tests/modules/nf-core/plink/indeppairwise/main.nf

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This file was deleted.

‎tests/modules/nf-core/plink/indeppairwise/nextflow.config

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This file was deleted.

‎tests/modules/nf-core/plink/indeppairwise/test.yml

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This file was deleted.

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