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Merge branch 'master' into workflows_of_workflows
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‎docs/nf4_science/genomics/04_testing.md‎

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‎mkdocs.yml‎

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- nf4_science/genomics/01_per_sample_variant_calling.md
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- nf4_science/genomics/02_joint_calling.md
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- nf4_science/genomics/03_modules.md
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- nf4_science/genomics/04_testing.md
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- Nextflow for RNAseq:
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- nf4_science/rnaseq/index.md
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- side_quests/nf-test.md
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- side_quests/workflows_of_workflows.md
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- nf4_science/genomics/03_modules.md
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- nf4_science/genomics/04_testing.md
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- i18n:
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docs_structure: suffix

‎nf4-science/genomics/solutions/modules/gatk/haplotypecaller/main.nf‎

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/*
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* Call variants with GATK HaplotypeCaller
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*/
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process GATK_HAPLOTYPECALLER {
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container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867"
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publishDir params.outdir, mode: 'symlink'
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input:
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tuple path(input_bam), path(input_bam_index)
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path ref_fasta
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path ref_index
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path ref_dict
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path interval_list
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output:
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path "${input_bam}.g.vcf" , emit: vcf
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path "${input_bam}.g.vcf.idx" , emit: idx
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script:
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"""
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gatk HaplotypeCaller \
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-R ${ref_fasta} \
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-I ${input_bam} \
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-O ${input_bam}.g.vcf \
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-L ${interval_list} \
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-ERC GVCF
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"""
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}

‎nf4-science/genomics/solutions/modules/gatk/haplotypecaller/tests/main.nf.test‎

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nextflow_process {
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name "Test Process GATK_HAPLOTYPECALLER"
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script "../main.nf"
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process "GATK_HAPLOTYPECALLER"
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test("Should call son's halotype correctly") {
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setup {
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run("SAMTOOLS_INDEX") {
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script "../../../samtools/index/main.nf"
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process {
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"""
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input[0] = file("${projectDir}/data/bam/reads_son.bam")
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"""
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}
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}
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}
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when {
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params {
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outdir = "tests/results"
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}
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process {
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"""
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input[0] = SAMTOOLS_INDEX.out
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input[1] = file("${projectDir}/data/ref/ref.fasta")
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input[2] = file("${projectDir}/data/ref/ref.fasta.fai")
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input[3] = file("${projectDir}/data/ref/ref.dict")
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input[4] = file("${projectDir}/data/ref/intervals.bed")
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"""
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}
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}
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then {
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assert process.success
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assert path(process.out[0][0]).readLines().contains('#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT reads_son')
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assert path(process.out[0][0]).readLines().contains('20_10037292_10066351 3277 . G <NON_REF> . . END=3282 GT:DP:GQ:MIN_DP:PL 0/0:25:72:24:0,72,719')
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}
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}
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test("Should call mother's halotype correctly") {
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setup {
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run("SAMTOOLS_INDEX") {
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script "../../../samtools/index/main.nf"
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process {
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"""
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input[0] = file("${projectDir}/data/bam/reads_mother.bam")
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"""
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}
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}
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}
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when {
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params {
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outdir = "tests/results"
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}
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process {
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"""
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input[0] = SAMTOOLS_INDEX.out
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input[1] = file("${projectDir}/data/ref/ref.fasta")
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input[2] = file("${projectDir}/data/ref/ref.fasta.fai")
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input[3] = file("${projectDir}/data/ref/ref.dict")
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input[4] = file("${projectDir}/data/ref/intervals.bed")
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"""
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}
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}
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then {
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assert process.success
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assert path(process.out[0][0]).readLines().contains('#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT reads_mother')
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assert path(process.out[0][0]).readLines().contains('20_10037292_10066351 3277 . G <NON_REF> . . END=3278 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,102,1530')
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}
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}
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test("Should call father's halotype correctly") {
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setup {
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run("SAMTOOLS_INDEX") {
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script "../../../samtools/index/main.nf"
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process {
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"""
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input[0] = file("${projectDir}/data/bam/reads_father.bam")
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"""
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}
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}
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}
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when {
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params {
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outdir = "tests/results"
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}
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process {
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"""
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input[0] = SAMTOOLS_INDEX.out
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input[1] = file("${projectDir}/data/ref/ref.fasta")
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input[2] = file("${projectDir}/data/ref/ref.fasta.fai")
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input[3] = file("${projectDir}/data/ref/ref.dict")
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input[4] = file("${projectDir}/data/ref/intervals.bed")
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"""
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}
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}
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then {
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assert process.success
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assert path(process.out[0][0]).readLines().contains('#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT reads_father')
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assert path(process.out[0][0]).readLines().contains('20_10037292_10066351 3277 . G <NON_REF> . . END=3281 GT:DP:GQ:MIN_DP:PL 0/0:44:99:42:0,120,1800')
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}
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}
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}

‎nf4-science/genomics/solutions/modules/gatk/haplotypecaller/tests/main.nf.test.snap‎

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{
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"Should call son's halotype correctly": {
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"content": [
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{
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"0": [
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"reads_son.bam.g.vcf:md5,069316cdd4328542ffc6ae247b1dac39"
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],
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"1": [
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"reads_son.bam.g.vcf.idx:md5,dc36c18f2afdc546f41e68b2687e9334"
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],
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"idx": [
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"reads_son.bam.g.vcf.idx:md5,dc36c18f2afdc546f41e68b2687e9334"
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],
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"vcf": [
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"reads_son.bam.g.vcf:md5,069316cdd4328542ffc6ae247b1dac39"
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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": "24.10.0"
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},
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"timestamp": "2025-03-04T09:26:58.537420116"
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}
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}

‎nf4-science/genomics/solutions/modules/gatk/jointgenotyping/main.nf‎

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/*
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* Combine GVCFs into GenomicsDB datastore and run joint genotyping to produce cohort-level calls
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*/
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process GATK_JOINTGENOTYPING {
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container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867"
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publishDir params.outdir, mode: 'copy'
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input:
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path all_gvcfs
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path all_idxs
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path interval_list
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val cohort_name
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path ref_fasta
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path ref_index
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path ref_dict
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output:
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path "${cohort_name}.joint.vcf" , emit: vcf
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path "${cohort_name}.joint.vcf.idx" , emit: idx
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script:
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def gvcfs_line = all_gvcfs.collect { gvcf -> "-V ${gvcf}" }.join(' ')
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"""
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gatk GenomicsDBImport \
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${gvcfs_line} \
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-L ${interval_list} \
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--genomicsdb-workspace-path ${cohort_name}_gdb
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gatk GenotypeGVCFs \
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-R ${ref_fasta} \
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-V gendb://${cohort_name}_gdb \
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-L ${interval_list} \
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-O ${cohort_name}.joint.vcf
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"""
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}

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