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test(gcta/makebksparse): generate GRM inputs in setup
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3 files changed

Lines changed: 72 additions & 45 deletions

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‎modules/nf-core/gcta/makebksparse/tests/helpers/dense_grm/main.nf‎

Lines changed: 33 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,33 @@
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process GCTA_TEST_DENSE_GRM {
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tag "${meta.id}"
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label "process_medium"
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conda "${projectDir}/modules/nf-core/gcta/makebksparse/environment.yml"
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container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'docker://community.wave.seqera.io/library/gcta:1.94.1--9bc35dc424fcf6e9' :
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'community.wave.seqera.io/library/gcta:1.94.1--9bc35dc424fcf6e9'}"
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input:
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tuple val(meta), path(bed), path(bim), path(fam)
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output:
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tuple val(meta), path("${meta.id}.grm.id"), path("${meta.id}.grm.bin"), path("${meta.id}.grm.N.bin"), emit: dense_grm
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script:
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def bfile_prefix = bed.baseName
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"""
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set -euo pipefail
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gcta \\
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--bfile "${bfile_prefix}" \\
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--make-grm \\
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--out "${meta.id}" \\
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--thread-num ${task.cpus}
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"""
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stub:
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"""
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touch "${meta.id}.grm.id"
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touch "${meta.id}.grm.bin"
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touch "${meta.id}.grm.N.bin"
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"""
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}

‎modules/nf-core/gcta/makebksparse/tests/main.nf.test‎

Lines changed: 36 additions & 42 deletions
Original file line numberDiff line numberDiff line change
@@ -8,29 +8,45 @@ nextflow_process {
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tag "modules_nfcore"
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tag "gcta"
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tag "gcta/makebksparse"
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tag "tests/helpers/dense_grm"
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setup {
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run("GCTA_TEST_DENSE_GRM", alias: "GCTA_TEST_DENSE_GRM_CONTRACT") {
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script "../tests/helpers/dense_grm/main.nf"
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process {
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"""
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input[0] = [
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[ id:'contract_dense' ],
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bed', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bim', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.fam', checkIfExists: true)
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]
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"""
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}
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}
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run("GCTA_TEST_DENSE_GRM", alias: "GCTA_TEST_DENSE_GRM_STUB") {
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script "../tests/helpers/dense_grm/main.nf"
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process {
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"""
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input[0] = [
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[ id:'stub_dense' ],
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bed', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bim', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.fam', 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("homo_sapiens popgen - create sparse GRM") {
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config "./nextflow.config"
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when {
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process {
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"""
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file('contract_dense.grm.id').text = "fid1 iid1\\n"
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grmBuffer = java.nio.ByteBuffer.allocate(4).order(java.nio.ByteOrder.LITTLE_ENDIAN)
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grmBuffer.putFloat(1.0f)
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file('contract_dense.grm.bin').bytes = grmBuffer.array()
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grmNBuffer = java.nio.ByteBuffer.allocate(4).order(java.nio.ByteOrder.LITTLE_ENDIAN)
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grmNBuffer.putFloat(100.0f)
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file('contract_dense.grm.N.bin').bytes = grmNBuffer.array()
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input[0] = Channel.value([
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[ id:'contract_dense' ],
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file('contract_dense.grm.id'),
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file('contract_dense.grm.bin'),
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file('contract_dense.grm.N.bin')
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])
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input[0] = GCTA_TEST_DENSE_GRM_CONTRACT.out.dense_grm
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input[1] = Channel.value(0.05)
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"""
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}
@@ -53,22 +69,9 @@ nextflow_process {
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when {
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process {
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"""
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file('contract_dense.grm.id').text = "fid1 iid1\\n"
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grmBuffer = java.nio.ByteBuffer.allocate(4).order(java.nio.ByteOrder.LITTLE_ENDIAN)
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grmBuffer.putFloat(1.0f)
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file('contract_dense.grm.bin').bytes = grmBuffer.array()
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grmNBuffer = java.nio.ByteBuffer.allocate(4).order(java.nio.ByteOrder.LITTLE_ENDIAN)
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grmNBuffer.putFloat(100.0f)
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file('contract_dense.grm.N.bin').bytes = grmNBuffer.array()
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input[0] = Channel.value([
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[ id:'contract_dense_mismatch' ],
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file('contract_dense.grm.id'),
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file('contract_dense.grm.bin'),
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file('contract_dense.grm.N.bin')
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])
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input[0] = GCTA_TEST_DENSE_GRM_CONTRACT.out.dense_grm.map { meta, grm_id, grm_bin, grm_n_bin ->
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[[ id:'contract_dense_mismatch' ], grm_id, grm_bin, grm_n_bin]
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}
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input[1] = Channel.value(0.05)
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"""
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}
@@ -89,16 +92,7 @@ nextflow_process {
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when {
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process {
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"""
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file('stub_dense.grm.id').text = "fid1 iid1\\n"
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file('stub_dense.grm.bin').bytes = []
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file('stub_dense.grm.N.bin').bytes = []
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input[0] = Channel.value([
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[ id:'stub_dense' ],
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file('stub_dense.grm.id'),
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file('stub_dense.grm.bin'),
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file('stub_dense.grm.N.bin')
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])
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input[0] = GCTA_TEST_DENSE_GRM_STUB.out.dense_grm
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input[1] = Channel.value(0.05)
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"""
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}

‎modules/nf-core/gcta/makebksparse/tests/main.nf.test.snap‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -42,16 +42,16 @@
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{
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"id": "contract_dense"
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},
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"contract_dense_sp.grm.id:md5,c1fd3a827b108cf8b749e4fced7b7a52",
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"contract_dense_sp.grm.sp:md5,9c1256f576632d254861b63586e7a3da"
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"contract_dense_sp.grm.id:md5,4f9aa36c44a417ff6d7caa9841e66ad9",
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"contract_dense_sp.grm.sp:md5,1b78fe4b14c8690943d7687dd22ba85a"
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]
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]
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],
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.4"
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},
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"timestamp": "2026-03-21T00:30:38.025448523"
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"timestamp": "2026-03-21T18:40:37.776832502"
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},
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"stub_versions": {
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"content": [

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