From 009f7c691c20f56e21e8b10907090384bfbad569 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Tue, 28 Jun 2022 09:44:08 +0100 Subject: [PATCH] Add module: gatk4/leftalignandtrimvariants (#1808) * Added: gatk4/leftalignandtrimvariants Additions: - GATK4/LeftAlignAndTrimVariants module - Use sars-ncov2 test data as this normalises a larger INDEL correctly. Fixes #1801 * fixup: Added index to output spec * fixup: Pattern of tbi output corrected to 'tbi' * gatk4/leftalignandtrimvariants: Added intervals Changes: - gatk4/leftalignandtrimvariants now supports optional interval as BED file - Tests added with and without interval. Not test BED file excludes all variants so no variants are actually normalised. Fixes #1801 * fixup: leftalignandtrimvariants vcf->tbi fix * fixup: gatk4/leftalignandtrimvariants Intervals added to meta.yml --- .../gatk4/leftalignandtrimvariants/main.nf | 48 +++++++++++++ .../gatk4/leftalignandtrimvariants/meta.yml | 69 +++++++++++++++++++ tests/config/pytest_modules.yml | 4 ++ .../gatk4/leftalignandtrimvariants/main.nf | 35 ++++++++++ .../leftalignandtrimvariants/nextflow.config | 9 +++ .../gatk4/leftalignandtrimvariants/test.yml | 22 ++++++ 6 files changed, 187 insertions(+) create mode 100644 modules/gatk4/leftalignandtrimvariants/main.nf create mode 100644 modules/gatk4/leftalignandtrimvariants/meta.yml create mode 100644 tests/modules/gatk4/leftalignandtrimvariants/main.nf create mode 100644 tests/modules/gatk4/leftalignandtrimvariants/nextflow.config create mode 100644 tests/modules/gatk4/leftalignandtrimvariants/test.yml diff --git a/modules/gatk4/leftalignandtrimvariants/main.nf b/modules/gatk4/leftalignandtrimvariants/main.nf new file mode 100644 index 00000000..1e3b8062 --- /dev/null +++ b/modules/gatk4/leftalignandtrimvariants/main.nf @@ -0,0 +1,48 @@ +process GATK4_LEFTALIGNANDTRIMVARIANTS { + tag "$meta.id" + label 'process_low' + + conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + + input: + tuple val(meta), path(vcf), path(tbi), path(intervals) + path fasta + path fai + path dict + + output: + tuple val(meta), path("*.vcf.gz"), emit: vcf + tuple val(meta), path("*.tbi") , emit: tbi + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def interval_command = intervals ? "--intervals $intervals" : "" + def avail_mem = 3 + if (!task.memory) { + log.info '[GATK LeftAlignAndTrimVariants] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' + } else { + avail_mem = task.memory.toGiga() + } + """ + gatk --java-options "-Xmx${avail_mem}G" LeftAlignAndTrimVariants \\ + $interval_command \\ + --variant $vcf \\ + --output ${prefix}.vcf.gz \\ + --reference $fasta \\ + --tmp-dir . \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ +} diff --git a/modules/gatk4/leftalignandtrimvariants/meta.yml b/modules/gatk4/leftalignandtrimvariants/meta.yml new file mode 100644 index 00000000..97b11097 --- /dev/null +++ b/modules/gatk4/leftalignandtrimvariants/meta.yml @@ -0,0 +1,69 @@ +name: "gatk4_leftalignandtrimvariants" +description: Left align and trim variants using GATK4 LeftAlignAndTrimVariants. +keywords: + - normalize + - norm + - vcf +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', single_end:false ] + - vcf: + type: file + description: | + The vcf file to be normalized + e.g. 'file1.vcf.gz' + - tbi: + type: file + description: | + Index of the vcf file to be normalized + e.g. 'file1.vcf.gz.tbi' + - intervals: + type: file + description: Bed file with the genomic regions included in the library (optional) + - 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" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - vcf: + type: file + description: VCF normalized output file + pattern: "*.{vcf.gz}" + - tbi: + type: file + description: Tbi index for VCF file + pattern: "*.tbi" +authors: + - "@adamrtalbot" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index d1a80f99..a6a37bb9 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -863,6 +863,10 @@ gatk4/learnreadorientationmodel: - modules/gatk4/learnreadorientationmodel/** - tests/modules/gatk4/learnreadorientationmodel/** +gatk4/leftalignandtrimvariants: + - modules/gatk4/leftalignandtrimvariants/** + - tests/modules/gatk4/leftalignandtrimvariants/** + gatk4/markduplicates: - modules/gatk4/markduplicates/** - tests/modules/gatk4/markduplicates/** diff --git a/tests/modules/gatk4/leftalignandtrimvariants/main.nf b/tests/modules/gatk4/leftalignandtrimvariants/main.nf new file mode 100644 index 00000000..1d890a54 --- /dev/null +++ b/tests/modules/gatk4/leftalignandtrimvariants/main.nf @@ -0,0 +1,35 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { GATK4_LEFTALIGNANDTRIMVARIANTS } from '../../../../modules/gatk4/leftalignandtrimvariants/main.nf' + +workflow test_gatk4_leftalignandtrimvariants_interval { + + input = [ [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true), + file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true), + ] + + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) + + GATK4_LEFTALIGNANDTRIMVARIANTS ( input, fasta, fai, dict ) +} + +workflow test_gatk4_leftalignandtrimvariants_no_interval { + + input = [ [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true), + [] + ] + + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) + + GATK4_LEFTALIGNANDTRIMVARIANTS ( input, fasta, fai, dict ) +} diff --git a/tests/modules/gatk4/leftalignandtrimvariants/nextflow.config b/tests/modules/gatk4/leftalignandtrimvariants/nextflow.config new file mode 100644 index 00000000..56fcee59 --- /dev/null +++ b/tests/modules/gatk4/leftalignandtrimvariants/nextflow.config @@ -0,0 +1,9 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + + withName: 'GATK4_LEFTALIGNANDTRIMVARIANTS' { + ext.args = "--split-multi-allelics --dont-trim-alleles --keep-original-ac" + ext.prefix = { "${meta.id}.normalised" } + } +} diff --git a/tests/modules/gatk4/leftalignandtrimvariants/test.yml b/tests/modules/gatk4/leftalignandtrimvariants/test.yml new file mode 100644 index 00000000..ff4ab0c4 --- /dev/null +++ b/tests/modules/gatk4/leftalignandtrimvariants/test.yml @@ -0,0 +1,22 @@ +- name: gatk4 leftalignandtrimvariants test_gatk4_leftalignandtrimvariants_interval + command: nextflow run ./tests/modules/gatk4/leftalignandtrimvariants -entry test_gatk4_leftalignandtrimvariants_interval -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/leftalignandtrimvariants/nextflow.config + tags: + - gatk4 + - gatk4/leftalignandtrimvariants + files: + - path: output/gatk4/test.normalised.vcf.gz + contains: + - "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT" + - path: output/gatk4/test.normalised.vcf.gz.tbi + +- name: gatk4 leftalignandtrimvariants test_gatk4_leftalignandtrimvariants_no_interval + command: nextflow run ./tests/modules/gatk4/leftalignandtrimvariants -entry test_gatk4_leftalignandtrimvariants_no_interval -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/leftalignandtrimvariants/nextflow.config + tags: + - gatk4 + - gatk4/leftalignandtrimvariants + files: + - path: output/gatk4/test.normalised.vcf.gz + contains: + - "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT" + - "MT192765.1\t10502\t.\tTAGATTATGACTGTGTCTCTTTTTGTTACATGCACCA\tTAGAT" + - path: output/gatk4/test.normalised.vcf.gz.tbi