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Add applyvqsr (#1101)
* 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 * add applyvqsr * added memory options, new test data used * Update main.nf * Update main.nf Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
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55
modules/gatk4/applyvqsr/main.nf
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55
modules/gatk4/applyvqsr/main.nf
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@ -0,0 +1,55 @@
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process GATK4_APPLYVQSR {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--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(vcf), path(tbi), path(recal), path(recalidx), path(tranches)
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path fasta
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path fai
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path dict
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val allelespecific
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val truthsensitivity
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val mode
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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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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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refCommand = fasta ? "-R ${fasta} " : ''
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alleleSpecificCommand = allelespecific ? '-AS' : ''
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truthSensitivityCommand = truthsensitivity ? "--truth-sensitivity-filter-level ${truthsensitivity}" : ''
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modeCommand = mode ? "--mode ${mode} " : 'SNP'
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def avail_mem = 3
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if (!task.memory) {
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log.info '[GATK ApplyVQSR] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
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} else {
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avail_mem = task.memory.giga
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}
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"""
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gatk --java-options "-Xmx${avail_mem}g" ApplyVQSR \\
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${refCommand} \\
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-V ${vcf} \\
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-O ${prefix}.vcf.gz \\
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${alleleSpecificCommand} \\
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${truthSensitivityCommand} \\
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--tranches-file $tranches \\
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--recal-file $recal \\
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${modeCommand} \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
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END_VERSIONS
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"""
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}
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88
modules/gatk4/applyvqsr/meta.yml
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88
modules/gatk4/applyvqsr/meta.yml
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@ -0,0 +1,88 @@
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name: gatk4_applyvqsr
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description: |
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Apply a score cutoff to filter variants based on a recalibration table.
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AplyVQSR performs the second pass in a two-stage process called Variant Quality Score Recalibration (VQSR).
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Specifically, it applies filtering to the input variants based on the recalibration table produced
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in the first step by VariantRecalibrator and a target sensitivity value.
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keywords:
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- gatk4
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- applyvqsr
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- VQSR
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tools:
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- gatk4:
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description: |
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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
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with a primary focus on variant discovery and genotyping. Its powerful processing engine
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and high-performance computing features make it capable of taking on projects of any size.
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homepage: https://gatk.broadinstitute.org/hc/en-us
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documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
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doi: 10.1158/1538-7445.AM2017-3590
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licence: ['Apache-2.0']
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test']
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- vcf:
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type: file
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description: VCF file to be recalibrated, this should be the same file as used for the first stage VariantRecalibrator.
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pattern: "*.vcf"
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- tbi:
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type: file
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description: Tbi index for the input vcf file.
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pattern: "*.vcf.tbi"
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- recal:
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type: file
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description: Recalibration file produced when the input vcf was run through VariantRecalibrator in stage 1.
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pattern: "*.recal"
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- recalidx:
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type: file
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description: Index file for the recalibration file.
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pattern: ".recal.idx"
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- tranches:
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type: boolean
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description: Tranches file produced when the input vcf was run through VariantRecalibrator in stage 1.
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pattern: ".tranches"
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- fasta:
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type: file
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description: The reference fasta file
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pattern: "*.fasta"
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- fai:
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type: file
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description: Index of reference fasta file
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pattern: "*.fasta.fai"
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- dict:
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type: file
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description: GATK sequence dictionary
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pattern: "*.dict"
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- allelespecific:
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type: boolean
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description: Whether or not to run ApplyVQSR in allele specific mode, this should be kept the same as the stage 1 VariantRecalibrator run.
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pattern: "{true,false}"
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- truthsensitivity:
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type: double
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description: Value to be used as the truth sensitivity cutoff score.
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pattern: "99.0"
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- mode:
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type: String
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description: Specifies which recalibration mode to employ, should be the same as the stage 1 VariantRecalibrator run. (SNP is default, BOTH is intended for testing only)
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pattern: "{SNP,INDEL,BOTH}"
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output:
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- vcf:
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type: file
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description: compressed vcf file containing the recalibrated variants.
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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 recalibrated 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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pattern: "versions.yml"
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authors:
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- "@GCJMackenzie"
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@ -504,6 +504,10 @@ gatk4/applybqsr:
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- modules/gatk4/applybqsr/**
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- tests/modules/gatk4/applybqsr/**
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gatk4/applyvqsr:
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- modules/gatk4/applyvqsr/**
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- tests/modules/gatk4/applyvqsr/**
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gatk4/baserecalibrator:
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- modules/gatk4/baserecalibrator/**
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- tests/modules/gatk4/baserecalibrator/**
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@ -115,6 +115,9 @@ params {
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transcriptome_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/transcriptome.fasta"
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genome2_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/genome2.fasta"
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genome_chain_gz = "${test_data_dir}/genomics/homo_sapiens/genome/genome.chain.gz"
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genome_21_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta"
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genome_21_fasta_fai = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai"
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genome_21_dict = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.dict"
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dbsnp_146_hg38_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz"
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dbsnp_146_hg38_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi"
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@ -122,6 +125,14 @@ params {
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gnomad_r2_1_1_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi"
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mills_and_1000g_indels_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz"
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mills_and_1000g_indels_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi"
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hapmap_3_3_hg38_21_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz"
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hapmap_3_3_hg38_21_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz.tbi"
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res_1000g_omni2_5_hg38_21_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz"
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res_1000g_omni2_5_hg38_21_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz.tbi"
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res_1000g_phase1_snps_hg38_21_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz"
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res_1000g_phase1_snps_hg38_21_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz.tbi"
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dbsnp_138_hg38_21_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz"
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dbsnp_138_hg38_21_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi"
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syntheticvcf_short_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz"
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syntheticvcf_short_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz.tbi"
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@ -197,6 +208,16 @@ params {
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test_genomicsdb_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz"
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test_pon_genomicsdb_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_pon_genomicsdb.tar.gz"
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test2_haplotc_ann_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz"
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test2_haplotc_ann_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi"
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test2_recal = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal"
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test2_recal_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal.idx"
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test2_tranches = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.tranches"
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test2_allele_specific_recal = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal"
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test2_allele_specific_recal_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal.idx"
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test2_allele_specific_tranches = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.tranches"
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test_test2_paired_mutect2_calls_vcf_gz = "${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 = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi"
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test_test2_paired_mutect2_calls_vcf_gz_stats = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.stats"
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41
tests/modules/gatk4/applyvqsr/main.nf
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41
tests/modules/gatk4/applyvqsr/main.nf
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GATK4_APPLYVQSR } from '../../../../modules/gatk4/applyvqsr/main.nf'
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workflow test_gatk4_applyvqsr {
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input = [ [ id:'test'], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_recal'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_recal_idx'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_tranches'], checkIfExists: true)
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
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fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
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dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
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allelespecific = false
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truthsensitivity = '99.0'
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mode = 'SNP'
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GATK4_APPLYVQSR ( input, fasta, fai, dict, allelespecific, truthsensitivity, mode )
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}
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workflow test_gatk4_applyvqsr_allele_specific {
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input = [ [ id:'test'], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_allele_specific_recal'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_allele_specific_recal_idx'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_allele_specific_tranches'], checkIfExists: true)
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
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fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
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dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
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allelespecific = true
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truthsensitivity = '99.0'
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mode = 'SNP'
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GATK4_APPLYVQSR ( input, fasta, fai, dict, allelespecific, truthsensitivity, mode )
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}
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5
tests/modules/gatk4/applyvqsr/nextflow.config
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5
tests/modules/gatk4/applyvqsr/nextflow.config
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process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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}
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17
tests/modules/gatk4/applyvqsr/test.yml
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17
tests/modules/gatk4/applyvqsr/test.yml
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- name: gatk4 applyvqsr test_gatk4_applyvqsr
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command: nextflow run tests/modules/gatk4/applyvqsr -entry test_gatk4_applyvqsr -c tests/config/nextflow.config -c ./tests/modules/gatk4/applyvqsr/nextflow.config
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tags:
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- gatk4
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- gatk4/applyvqsr
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files:
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- path: output/gatk4/test.vcf.gz
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- path: output/gatk4/test.vcf.gz.tbi
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- name: gatk4 applyvqsr test_gatk4_applyvqsr_allele_specific
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command: nextflow run tests/modules/gatk4/applyvqsr -entry test_gatk4_applyvqsr_allele_specific -c tests/config/nextflow.config -c ./tests/modules/gatk4/applyvqsr/nextflow.config
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tags:
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- gatk4
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- gatk4/applyvqsr
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files:
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- path: output/gatk4/test.vcf.gz
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- path: output/gatk4/test.vcf.gz.tbi
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