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Update in GATK4 variantfiltration: Added vcf_index to vcf tuple; output to vcf.gz format. (#1083)
* Added vcf_index to vcf tuple; output to vcf.gz format. * Fix: extra new line in meta.yml. * addressed review feedback * fix: editorconfig error * fix: gatk memory flag * fix: editorconfig error * fix: Indentation fix: Indentation * Fix: lint editorconfig error Removed one extra space Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
This commit is contained in:
praveenraj2018
GitHub
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commit
43a1c1c6d1
4 changed files with 65 additions and 23 deletions
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@ -19,23 +19,29 @@ process GATK4_VARIANTFILTRATION {
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}
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input:
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tuple val(meta), path(vcf)
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tuple val(meta), path(vcf), path(vcf_tbi)
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path fasta
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path fai
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path dict
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output:
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tuple val(meta), path("*.vcf"), emit: vcf
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path "versions.yml" , emit: versions
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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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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def avail_mem = 3
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if (!task.memory) {
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log.info '[GATK HaplotypeCaller] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
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} else {
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avail_mem = task.memory.toGiga()
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}
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"""
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gatk VariantFiltration \\
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gatk --java-options "-Xmx${avail_mem}G" VariantFiltration \\
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-R $fasta \\
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-V $vcf \\
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-O ${prefix}.vcf \\
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-O ${prefix}.vcf.gz \\
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$options.args
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cat <<-END_VERSIONS > versions.yml
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@ -21,8 +21,12 @@ input:
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e.g. [ id:'test']
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- vcf:
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type: list
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description: Input VCF file
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pattern: "*.{vcf}"
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description: List of VCF(.gz) files
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pattern: "*.{vcf,vcf.gz}"
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- vcf_tbi:
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type: list
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description: List of VCF file indexes
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pattern: "*.{idx,tbi}"
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- fasta:
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type: file
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description: Fasta file of reference genome
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@ -38,8 +42,12 @@ input:
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output:
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- vcf:
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type: file
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description: filtered VCF file
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pattern: "*.filtered.{vcf}"
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description: Compressed 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: Index of VCF file
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pattern: "*.vcf.gz.tbi"
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- versions:
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type: file
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description: File containing software versions
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@ -5,14 +5,32 @@ nextflow.enable.dsl = 2
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test_options = ['args': '--filter-name "test_filter" --filter-expression "MQ0 > 0"', 'suffix': '.filtered']
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include { GATK4_VARIANTFILTRATION } from '../../../../modules/gatk4/variantfiltration/main.nf' addParams( options: test_options )
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workflow test_gatk4_variantfiltration {
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// Basic parameters with uncompressed VCF input
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workflow test_gatk4_variantfiltration_vcf_input {
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input = [ [ id:'test' ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
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]
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fasta = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
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fai = [ file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ]
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genome_dict = [ file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ]
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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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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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GATK4_VARIANTFILTRATION ( input, fasta, fai, genome_dict )
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GATK4_VARIANTFILTRATION ( input, fasta, fastaIndex, fastaDict )
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}
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// Basic parameters with compressed VCF input
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workflow test_gatk4_variantfiltration_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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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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GATK4_VARIANTFILTRATION ( input, fasta, fastaIndex, fastaDict )
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}
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@ -1,9 +1,19 @@
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- name: gatk4 variantfiltration test_gatk4_variantfiltration
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command: nextflow run tests/modules/gatk4/variantfiltration -entry test_gatk4_variantfiltration -c tests/config/nextflow.config
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- name: gatk4 variantfiltration test_gatk4_variantfiltration_vcf_input
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command: nextflow run tests/modules/gatk4/variantfiltration -entry test_gatk4_variantfiltration_vcf_input -c tests/config/nextflow.config
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tags:
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- gatk4/variantfiltration
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- gatk4
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files:
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- path: output/gatk4/test.filtered.vcf
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contains:
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- "AC=2;AN=2;DP=1;DP4=0,0,1,0;MQ=60;MQ0F=0;SGB=-0.379885"
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- path: output/gatk4/test.filtered.vcf.gz
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contains: ['BaseQRankSum=-1.318;DP=17;ExcessHet=3.0103;MLEAC=1,0,0;MLEAF=0.500,0.00,0.00;MQRankSum=0.000;RAW_MQandDP=61200,17;ReadPosRankSum=2.365']
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- path: output/gatk4/test.filtered.vcf.gz.tbi
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- name: gatk4 variantfiltration test_gatk4_variantfiltration_gz_input
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command: nextflow run tests/modules/gatk4/variantfiltration -entry test_gatk4_variantfiltration_gz_input -c tests/config/nextflow.config
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tags:
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- gatk4/variantfiltration
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- gatk4
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files:
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- path: output/gatk4/test.filtered.vcf.gz
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contains: ['BaseQRankSum=-1.318;DP=17;ExcessHet=3.0103;MLEAC=1,0,0;MLEAF=0.500,0.00,0.00;MQRankSum=0.000;RAW_MQandDP=61200,17;ReadPosRankSum=2.365']
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- path: output/gatk4/test.filtered.vcf.gz.tbi
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