mirror of
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BugFix: add missing tbi output channel to genotypeGVCFs (#1153)
* initial commit to setup branch * workflow finished * Update nextflow.config * tumour to tumor, getpileup passed as nomral and tumor * paired_somatic renamed to tumor_normal_somatic * Apply suggestions from code review Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * Update subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/main.nf Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * updated index names in meta.yml * changed index file names in main script and test * Apply suggestions from code review Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * Apply suggestions from code review * fixed bug from changes * Apply suggestions from code review * modified yml to allow new subworkflow testing * Update test.yml * Update test.yml * added output channel for tbi files, tweaked method of adding blank inputs for gendb tests * Update main.nf * Update main.nf Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
This commit is contained in:
GCJMackenzie
GitHub
parent
4e5406c221
commit
61376425fb
5 changed files with 38 additions and 40 deletions
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@ -2,10 +2,10 @@ process GATK4_GENOTYPEGVCFS {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
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conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0' :
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'quay.io/biocontainers/gatk4:4.2.0.0--0' }"
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
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'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
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input:
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tuple val(meta), path(gvcf), path(gvcf_index)
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@ -18,6 +18,7 @@ process GATK4_GENOTYPEGVCFS {
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output:
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tuple val(meta), path("*.vcf.gz"), emit: vcf
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tuple val(meta), path("*.tbi") , emit: tbi
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path "versions.yml" , emit: versions
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script:
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@ -60,6 +60,10 @@ output:
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type: file
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description: Genotyped VCF file
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pattern: "*.vcf.gz"
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- tbi:
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type: file
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description: Tbi index for VCF file
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pattern: "*.vcf.gz"
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- versions:
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type: file
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description: File containing software versions
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@ -193,9 +193,9 @@ params {
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test2_baserecalibrator_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.baserecalibrator.table"
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test_pileups_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.pileups.table"
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test2_pileups_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.pileups.table"
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test_genomicsdb_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz"
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test_genomicsdb_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz"
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test_pon_genomicsdb_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_pon_genomicsdb.tar.gz"
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test_test2_paired_mutect2_calls_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz"
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test_test2_paired_mutect2_calls_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi"
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@ -7,7 +7,7 @@ include { UNTAR } from '../../../../modules/untar/main.nf'
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// Basic parameters with uncompressed VCF input
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workflow test_gatk4_genotypegvcfs_vcf_input {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_idx'], checkIfExists: true) ]
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@ -21,7 +21,7 @@ workflow test_gatk4_genotypegvcfs_vcf_input {
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// Basic parameters with compressed VCF input
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workflow test_gatk4_genotypegvcfs_gz_input {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true) ]
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@ -35,7 +35,7 @@ workflow test_gatk4_genotypegvcfs_gz_input {
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// Basic parameters + optional dbSNP
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workflow test_gatk4_genotypegvcfs_gz_input_dbsnp {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true) ]
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@ -52,7 +52,7 @@ workflow test_gatk4_genotypegvcfs_gz_input_dbsnp {
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// Basic parameters + optional intervals
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workflow test_gatk4_genotypegvcfs_gz_input_intervals {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true) ]
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@ -68,7 +68,7 @@ workflow test_gatk4_genotypegvcfs_gz_input_intervals {
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// Basic parameters + optional dbSNP + optional intervals
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workflow test_gatk4_genotypegvcfs_gz_input_dbsnp_intervals {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true) ]
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@ -95,20 +95,16 @@ workflow test_gatk4_genotypegvcfs_gendb_input {
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test_genomicsdb = file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true)
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UNTAR ( test_genomicsdb )
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Channel.of(file("mock_gvcf_index.txt")).set{mock_gvcf_index}
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Channel
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.of([ id:'test' ])
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.combine(UNTAR.out.untar)
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.combine(mock_gvcf_index)
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.set{ input }
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gendb = UNTAR.out.untar.collect()
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gendb.add([])
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input = Channel.of([ id:'test' ]).combine(gendb)
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GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, [], [], [] )
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}
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// Basic parameters with GenomicsDB + optional dbSNP
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workflow test_gatk4_genotypegvcfs_gendb_input_dbsnp {
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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fastaIndex = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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fastaDict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
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@ -119,20 +115,16 @@ workflow test_gatk4_genotypegvcfs_gendb_input_dbsnp {
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test_genomicsdb = file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true)
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UNTAR ( test_genomicsdb )
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Channel.of(file("mock_gvcf_index.txt")).set{mock_gvcf_index}
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Channel
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.of([ id:'test' ])
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.combine(UNTAR.out.untar)
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.combine(mock_gvcf_index)
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.set{ input }
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gendb = UNTAR.out.untar.collect()
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gendb.add([])
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input = Channel.of([ id:'test' ]).combine(gendb)
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GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, dbsnp, dbsnpIndex, [] )
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}
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// Basic parameters with GenomicsDB + optional intervals
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workflow test_gatk4_genotypegvcfs_gendb_input_intervals {
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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fastaIndex = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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fastaDict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
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@ -142,20 +134,16 @@ workflow test_gatk4_genotypegvcfs_gendb_input_intervals {
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test_genomicsdb = file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true)
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UNTAR ( test_genomicsdb )
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Channel.of(file("mock_gvcf_index.txt")).set{mock_gvcf_index}
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Channel
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.of([ id:'test' ])
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.combine(UNTAR.out.untar)
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.combine(mock_gvcf_index)
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.set{ input }
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gendb = UNTAR.out.untar.collect()
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gendb.add([])
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input = Channel.of([ id:'test' ]).combine(gendb)
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GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, [], [], intervalsBed )
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}
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// Basic parameters with GenomicsDB + optional dbSNP + optional intervals
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workflow test_gatk4_genotypegvcfs_gendb_input_dbsnp_intervals {
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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fastaIndex = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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fastaDict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
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@ -168,13 +156,9 @@ workflow test_gatk4_genotypegvcfs_gendb_input_dbsnp_intervals {
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test_genomicsdb = file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true)
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UNTAR ( test_genomicsdb )
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Channel.of(file("mock_gvcf_index.txt")).set{mock_gvcf_index}
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Channel
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.of([ id:'test' ])
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.combine(UNTAR.out.untar)
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.combine(mock_gvcf_index)
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.set{ input }
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gendb = UNTAR.out.untar.collect()
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gendb.add([])
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input = Channel.of([ id:'test' ]).combine(gendb)
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GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, dbsnp, dbsnpIndex, intervalsBed )
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}
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@ -6,6 +6,7 @@
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files:
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- path: output/gatk4/test.genotyped.vcf.gz
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contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
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- path: output/gatk4/test.genotyped.vcf.gz.tbi
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- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input
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command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gz_input -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
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@ -15,6 +16,7 @@
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files:
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- path: output/gatk4/test.genotyped.vcf.gz
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contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
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- path: output/gatk4/test.genotyped.vcf.gz.tbi
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- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input_dbsnp
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command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gz_input_dbsnp -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
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@ -24,6 +26,7 @@
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files:
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- path: output/gatk4/test.genotyped.vcf.gz
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contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DB;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
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- path: output/gatk4/test.genotyped.vcf.gz.tbi
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- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input_intervals
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command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gz_input_intervals -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
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@ -33,6 +36,7 @@
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files:
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- path: output/gatk4/test.genotyped.vcf.gz
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contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
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- path: output/gatk4/test.genotyped.vcf.gz.tbi
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- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input_dbsnp_intervals
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command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gz_input_dbsnp_intervals -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
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@ -42,6 +46,7 @@
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files:
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- path: output/gatk4/test.genotyped.vcf.gz
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contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DB;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
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- path: output/gatk4/test.genotyped.vcf.gz.tbi
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- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input
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command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gendb_input -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
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@ -51,6 +56,7 @@
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files:
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- path: output/gatk4/test.genotyped.vcf.gz
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contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
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- path: output/gatk4/test.genotyped.vcf.gz.tbi
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- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input_dbsnp
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command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gendb_input_dbsnp -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
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@ -60,6 +66,7 @@
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files:
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- path: output/gatk4/test.genotyped.vcf.gz
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contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DB;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
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- path: output/gatk4/test.genotyped.vcf.gz.tbi
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- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input_intervals
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command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gendb_input_intervals -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
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@ -69,6 +76,7 @@
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files:
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- path: output/gatk4/test.genotyped.vcf.gz
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contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
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- path: output/gatk4/test.genotyped.vcf.gz.tbi
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- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input_dbsnp_intervals
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command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gendb_input_dbsnp_intervals -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
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@ -78,3 +86,4 @@
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files:
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- path: output/gatk4/test.genotyped.vcf.gz
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contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DB;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
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- path: output/gatk4/test.genotyped.vcf.gz.tbi
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