From 9f8d9fb615bdb45a164e9dd59bb35043b99f5ae0 Mon Sep 17 00:00:00 2001 From: GCJMackenzie <43276267+GCJMackenzie@users.noreply.github.com> Date: Thu, 16 Dec 2021 08:44:50 +0000 Subject: [PATCH] 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 * Update subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/main.nf Co-authored-by: Maxime U. Garcia * 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 * 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 Co-authored-by: Maxime U. Garcia --- modules/gatk4/applyvqsr/main.nf | 55 ++++++++++++ modules/gatk4/applyvqsr/meta.yml | 88 +++++++++++++++++++ tests/config/pytest_modules.yml | 4 + tests/config/test_data.config | 21 +++++ tests/modules/gatk4/applyvqsr/main.nf | 41 +++++++++ tests/modules/gatk4/applyvqsr/nextflow.config | 5 ++ tests/modules/gatk4/applyvqsr/test.yml | 17 ++++ 7 files changed, 231 insertions(+) create mode 100644 modules/gatk4/applyvqsr/main.nf create mode 100644 modules/gatk4/applyvqsr/meta.yml create mode 100644 tests/modules/gatk4/applyvqsr/main.nf create mode 100644 tests/modules/gatk4/applyvqsr/nextflow.config create mode 100644 tests/modules/gatk4/applyvqsr/test.yml diff --git a/modules/gatk4/applyvqsr/main.nf b/modules/gatk4/applyvqsr/main.nf new file mode 100644 index 00000000..89f79f42 --- /dev/null +++ b/modules/gatk4/applyvqsr/main.nf @@ -0,0 +1,55 @@ +process GATK4_APPLYVQSR { + tag "$meta.id" + label 'process_low' + + conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }" + + input: + tuple val(meta), path(vcf), path(tbi), path(recal), path(recalidx), path(tranches) + path fasta + path fai + path dict + val allelespecific + val truthsensitivity + val mode + + output: + tuple val(meta), path("*.vcf.gz") , emit: vcf + tuple val(meta), path("*.tbi") , emit: tbi + path "versions.yml" , emit: versions + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + refCommand = fasta ? "-R ${fasta} " : '' + alleleSpecificCommand = allelespecific ? '-AS' : '' + truthSensitivityCommand = truthsensitivity ? "--truth-sensitivity-filter-level ${truthsensitivity}" : '' + modeCommand = mode ? "--mode ${mode} " : 'SNP' + + def avail_mem = 3 + if (!task.memory) { + log.info '[GATK ApplyVQSR] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' + } else { + avail_mem = task.memory.giga + } + """ + gatk --java-options "-Xmx${avail_mem}g" ApplyVQSR \\ + ${refCommand} \\ + -V ${vcf} \\ + -O ${prefix}.vcf.gz \\ + ${alleleSpecificCommand} \\ + ${truthSensitivityCommand} \\ + --tranches-file $tranches \\ + --recal-file $recal \\ + ${modeCommand} \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ +} diff --git a/modules/gatk4/applyvqsr/meta.yml b/modules/gatk4/applyvqsr/meta.yml new file mode 100644 index 00000000..b757f3e9 --- /dev/null +++ b/modules/gatk4/applyvqsr/meta.yml @@ -0,0 +1,88 @@ +name: gatk4_applyvqsr +description: | + Apply a score cutoff to filter variants based on a recalibration table. + AplyVQSR performs the second pass in a two-stage process called Variant Quality Score Recalibration (VQSR). + Specifically, it applies filtering to the input variants based on the recalibration table produced + in the first step by VariantRecalibrator and a target sensitivity value. +keywords: + - gatk4 + - applyvqsr + - VQSR +tools: + - gatk4: + description: | + Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools + with a primary focus on variant discovery and genotyping. Its powerful processing engine + and high-performance computing features make it capable of taking on projects of any size. + homepage: https://gatk.broadinstitute.org/hc/en-us + documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s + doi: 10.1158/1538-7445.AM2017-3590 + licence: ['Apache-2.0'] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - vcf: + type: file + description: VCF file to be recalibrated, this should be the same file as used for the first stage VariantRecalibrator. + pattern: "*.vcf" + - tbi: + type: file + description: Tbi index for the input vcf file. + pattern: "*.vcf.tbi" + - recal: + type: file + description: Recalibration file produced when the input vcf was run through VariantRecalibrator in stage 1. + pattern: "*.recal" + - recalidx: + type: file + description: Index file for the recalibration file. + pattern: ".recal.idx" + - tranches: + type: boolean + description: Tranches file produced when the input vcf was run through VariantRecalibrator in stage 1. + pattern: ".tranches" + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" + - allelespecific: + type: boolean + description: Whether or not to run ApplyVQSR in allele specific mode, this should be kept the same as the stage 1 VariantRecalibrator run. + pattern: "{true,false}" + - truthsensitivity: + type: double + description: Value to be used as the truth sensitivity cutoff score. + pattern: "99.0" + - mode: + type: String + 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) + pattern: "{SNP,INDEL,BOTH}" + +output: + - vcf: + type: file + description: compressed vcf file containing the recalibrated variants. + pattern: "*.vcf.gz" + - tbi: + type: file + description: Index of recalibrated vcf file. + pattern: "*vcf.gz.tbi" + - versions: + type: file + description: File containing software versions. + pattern: "versions.yml" + +authors: + - "@GCJMackenzie" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index cc4356a7..c261a481 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -504,6 +504,10 @@ gatk4/applybqsr: - modules/gatk4/applybqsr/** - tests/modules/gatk4/applybqsr/** +gatk4/applyvqsr: + - modules/gatk4/applyvqsr/** + - tests/modules/gatk4/applyvqsr/** + gatk4/baserecalibrator: - modules/gatk4/baserecalibrator/** - tests/modules/gatk4/baserecalibrator/** diff --git a/tests/config/test_data.config b/tests/config/test_data.config index b2edcb6f..fddc4489 100644 --- a/tests/config/test_data.config +++ b/tests/config/test_data.config @@ -115,6 +115,9 @@ params { transcriptome_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/transcriptome.fasta" genome2_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/genome2.fasta" genome_chain_gz = "${test_data_dir}/genomics/homo_sapiens/genome/genome.chain.gz" + genome_21_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta" + genome_21_fasta_fai = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai" + genome_21_dict = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.dict" dbsnp_146_hg38_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz" dbsnp_146_hg38_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi" @@ -122,6 +125,14 @@ params { gnomad_r2_1_1_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi" mills_and_1000g_indels_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz" mills_and_1000g_indels_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi" + hapmap_3_3_hg38_21_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz" + hapmap_3_3_hg38_21_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz.tbi" + res_1000g_omni2_5_hg38_21_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz" + res_1000g_omni2_5_hg38_21_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz.tbi" + res_1000g_phase1_snps_hg38_21_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz" + res_1000g_phase1_snps_hg38_21_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz.tbi" + dbsnp_138_hg38_21_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz" + dbsnp_138_hg38_21_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi" syntheticvcf_short_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz" syntheticvcf_short_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz.tbi" @@ -197,6 +208,16 @@ params { test_genomicsdb_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz" test_pon_genomicsdb_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_pon_genomicsdb.tar.gz" + test2_haplotc_ann_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz" + test2_haplotc_ann_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi" + + test2_recal = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal" + test2_recal_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal.idx" + test2_tranches = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.tranches" + test2_allele_specific_recal = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal" + test2_allele_specific_recal_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal.idx" + test2_allele_specific_tranches = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.tranches" + test_test2_paired_mutect2_calls_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz" test_test2_paired_mutect2_calls_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi" test_test2_paired_mutect2_calls_vcf_gz_stats = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.stats" diff --git a/tests/modules/gatk4/applyvqsr/main.nf b/tests/modules/gatk4/applyvqsr/main.nf new file mode 100644 index 00000000..90a57aaa --- /dev/null +++ b/tests/modules/gatk4/applyvqsr/main.nf @@ -0,0 +1,41 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { GATK4_APPLYVQSR } from '../../../../modules/gatk4/applyvqsr/main.nf' + +workflow test_gatk4_applyvqsr { + input = [ [ id:'test'], // meta map + file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_recal'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_recal_idx'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_tranches'], checkIfExists: true) + ] + fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) + dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) + allelespecific = false + truthsensitivity = '99.0' + mode = 'SNP' + + GATK4_APPLYVQSR ( input, fasta, fai, dict, allelespecific, truthsensitivity, mode ) +} + +workflow test_gatk4_applyvqsr_allele_specific { + input = [ [ id:'test'], // meta map + file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_allele_specific_recal'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_allele_specific_recal_idx'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_allele_specific_tranches'], checkIfExists: true) + ] + fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) + dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) + allelespecific = true + truthsensitivity = '99.0' + mode = 'SNP' + + GATK4_APPLYVQSR ( input, fasta, fai, dict, allelespecific, truthsensitivity, mode ) +} diff --git a/tests/modules/gatk4/applyvqsr/nextflow.config b/tests/modules/gatk4/applyvqsr/nextflow.config new file mode 100644 index 00000000..19934e76 --- /dev/null +++ b/tests/modules/gatk4/applyvqsr/nextflow.config @@ -0,0 +1,5 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + +} \ No newline at end of file diff --git a/tests/modules/gatk4/applyvqsr/test.yml b/tests/modules/gatk4/applyvqsr/test.yml new file mode 100644 index 00000000..e870bed3 --- /dev/null +++ b/tests/modules/gatk4/applyvqsr/test.yml @@ -0,0 +1,17 @@ +- name: gatk4 applyvqsr test_gatk4_applyvqsr + command: nextflow run tests/modules/gatk4/applyvqsr -entry test_gatk4_applyvqsr -c tests/config/nextflow.config -c ./tests/modules/gatk4/applyvqsr/nextflow.config + tags: + - gatk4 + - gatk4/applyvqsr + files: + - path: output/gatk4/test.vcf.gz + - path: output/gatk4/test.vcf.gz.tbi + +- name: gatk4 applyvqsr test_gatk4_applyvqsr_allele_specific + 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 + tags: + - gatk4 + - gatk4/applyvqsr + files: + - path: output/gatk4/test.vcf.gz + - path: output/gatk4/test.vcf.gz.tbi