From 7676d9d7282c74a429ed08962db5556295f17108 Mon Sep 17 00:00:00 2001 From: GCJMackenzie <43276267+GCJMackenzie@users.noreply.github.com> Date: Sat, 23 Oct 2021 18:45:19 +0100 Subject: [PATCH] Filtermutectcalls (#796) * first commit with files for filtermutectcalls initialised * found missing test file that needs to be resolved * saving config changes * fixing pytest_module conflict * finished module, just needs repository side tests added * test data added, versions file updated * modified to emit correct versions file * Update main.nf * Update test_data.config * updated test script * fixed main.nf * Update main.nf * Update main.nf * removed whitespace from test script * Update test_data.config * Update .gitignore * Update test_data.config * tests changed to new names, main script edited to match comments on learnreads pr * Update meta.yml * Apply suggestions from code review * Update main.nf * Apply suggestions from code review * Apply suggestions from code review * Update main.nf * Update main.nf * Update main.nf * Update main.nf Co-authored-by: GCJMackenzie Co-authored-by: James A. Fellows Yates Co-authored-by: Harshil Patel --- modules/gatk4/filtermutectcalls/functions.nf | 78 +++++++++++++++++ modules/gatk4/filtermutectcalls/main.nf | 65 ++++++++++++++ modules/gatk4/filtermutectcalls/meta.yml | 84 +++++++++++++++++++ tests/config/pytest_modules.yml | 4 + tests/modules/gatk4/filtermutectcalls/main.nf | 65 ++++++++++++++ .../modules/gatk4/filtermutectcalls/test.yml | 35 ++++++++ 6 files changed, 331 insertions(+) create mode 100644 modules/gatk4/filtermutectcalls/functions.nf create mode 100644 modules/gatk4/filtermutectcalls/main.nf create mode 100644 modules/gatk4/filtermutectcalls/meta.yml create mode 100644 tests/modules/gatk4/filtermutectcalls/main.nf create mode 100644 tests/modules/gatk4/filtermutectcalls/test.yml diff --git a/modules/gatk4/filtermutectcalls/functions.nf b/modules/gatk4/filtermutectcalls/functions.nf new file mode 100644 index 00000000..85628ee0 --- /dev/null +++ b/modules/gatk4/filtermutectcalls/functions.nf @@ -0,0 +1,78 @@ +// +// Utility functions used in nf-core DSL2 module files +// + +// +// Extract name of software tool from process name using $task.process +// +def getSoftwareName(task_process) { + return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() +} + +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + +// +// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules +// +def initOptions(Map args) { + def Map options = [:] + options.args = args.args ?: '' + options.args2 = args.args2 ?: '' + options.args3 = args.args3 ?: '' + options.publish_by_meta = args.publish_by_meta ?: [] + options.publish_dir = args.publish_dir ?: '' + options.publish_files = args.publish_files + options.suffix = args.suffix ?: '' + return options +} + +// +// Tidy up and join elements of a list to return a path string +// +def getPathFromList(path_list) { + def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries + paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes + return paths.join('/') +} + +// +// Function to save/publish module results +// +def saveFiles(Map args) { + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] + } + path = path instanceof String ? path : '' + path_list.add(path) + } + } + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" + } +} diff --git a/modules/gatk4/filtermutectcalls/main.nf b/modules/gatk4/filtermutectcalls/main.nf new file mode 100644 index 00000000..5a784677 --- /dev/null +++ b/modules/gatk4/filtermutectcalls/main.nf @@ -0,0 +1,65 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' + +params.options = [:] +options = initOptions(params.options) + +process GATK4_FILTERMUTECTCALLS { + tag "$meta.id" + label 'process_low' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } + + conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0" + } else { + container "quay.io/biocontainers/gatk4:4.2.0.0--0" + } + + input: + tuple val(meta), path(vcf), path(tbi), path(stats), path(orientationbias), path(segmentation), path(contaminationfile), val(contaminationest) + path fasta + path fastaidx + path dict + + output: + tuple val(meta), path("*.vcf.gz") , emit: vcf + tuple val(meta), path("*.vcf.gz.tbi") , emit: tbi + tuple val(meta), path("*.filteringStats.tsv"), emit: stats + path "versions.yml" , emit: versions + + script: + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + + def orientationbias_options = '' + if (orientationbias) { + orientationbias_options = '--orientation-bias-artifact-priors ' + orientationbias.join(' --orientation-bias-artifact-priors ') + } + + def segmentation_options = '' + if (segmentation) { + segmentation_options = '--tumor-segmentation ' + segmentation.join(' --tumor-segmentation ') + } + + def contamination_options = contaminationest ? " --contamination-estimate ${contaminationest} " : '' + if (contaminationfile) { + contamination_options = '--contamination-table ' + contaminationfile.join(' --contamination-table ') + } + """ + gatk FilterMutectCalls \\ + -R $fasta \\ + -V $vcf \\ + $orientationbias_options \\ + $segmentation_options \\ + $contamination_options \\ + -O ${prefix}.vcf.gz \\ + $options.args + + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ +} diff --git a/modules/gatk4/filtermutectcalls/meta.yml b/modules/gatk4/filtermutectcalls/meta.yml new file mode 100644 index 00000000..f14f9404 --- /dev/null +++ b/modules/gatk4/filtermutectcalls/meta.yml @@ -0,0 +1,84 @@ +name: gatk4_filtermutectcalls +description: | + Filters the raw output of mutect2, can optionally use outputs of calculatecontamination and learnreadorientationmodel to improve filtering. +keywords: + - filtermutectcalls + - mutect2 + - gatk4 + - filtervcf +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 + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - vcf: + type: file + description: compressed vcf file of mutect2calls + pattern: "*.vcf.gz" + - tbi: + type: file + description: Index of vcf file + pattern: "*vcf.gz.tbi" + - stats: + type: file + description: Stats file that pairs with output vcf file + pattern: "*vcf.gz.stats" + - orientationbias: + type: list + description: files containing artifact priors for input vcf. Optional input. + pattern: "*.artifact-prior.tar.gz" + - segmentation: + type: list + description: tables containing segmentation information for input vcf. Optional input. + pattern: "*.segmentation.table" + - contaminationfile: + type: list + description: table(s) containing contamination contamination data for input vcf. Optional input, takes priority over contaminationest. + pattern: "*.contamination.table" + - contaminationest: + type: val + description: estimation of contamination value as a double. Optional input, will only be used if contaminationfile is not specified. + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - fastaidx: + type: file + description: Index of reference fasta file + pattern: "fasta.fai" + - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" + +output: + - vcf: + type: file + description: file containing filtered mutect2 calls. + pattern: "*.vcf.gz" + - tbi: + type: file + description: tbi file that pairs with vcf. + pattern: "*.vcf.gz.tbi" + - stats: + type: file + description: file containing statistics of the filtermutectcalls run. + pattern: "*.filteringStats.tsv" + - 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 7093790b..dfa00bd0 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -410,6 +410,10 @@ gatk4/fastqtosam: - modules/gatk4/fastqtosam/** - tests/modules/gatk4/fastqtosam/** +gatk4/filtermutectcalls: + - modules/gatk4/filtermutectcalls/** + - tests/modules/gatk4/filtermutectcalls/** + gatk4/getpileupsummaries: - modules/gatk4/getpileupsummaries/** - tests/modules/gatk4/getpileupsummaries/** diff --git a/tests/modules/gatk4/filtermutectcalls/main.nf b/tests/modules/gatk4/filtermutectcalls/main.nf new file mode 100644 index 00000000..a425238b --- /dev/null +++ b/tests/modules/gatk4/filtermutectcalls/main.nf @@ -0,0 +1,65 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { GATK4_FILTERMUTECTCALLS } from '../../../../modules/gatk4/filtermutectcalls/main.nf' addParams( options: [suffix:'.filtered'] ) + +workflow test_gatk4_filtermutectcalls_base { + + input = [ + [ id:'test'], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_tbi'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_stats'], checkIfExists: true), + [], + [], + [], + [] + ] + + fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + + GATK4_FILTERMUTECTCALLS ( input, fasta, fastaidx, dict ) +} + +workflow test_gatk4_filtermutectcalls_with_files { + + input = [ + [ id:'test'], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_tbi'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_stats'], checkIfExists: true), + [ file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_artifact_prior_tar_gz'], checkIfExists: true) ], + [ file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_segmentation_table'], checkIfExists: true) ], + [ file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_contamination_table'], checkIfExists: true) ], + [] + ] + + fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + + GATK4_FILTERMUTECTCALLS ( input, fasta, fastaidx, dict ) +} + +workflow test_gatk4_filtermutectcalls_use_val { + + input = [ + [ id:'test'], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_tbi'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_stats'], checkIfExists: true), + [ file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_artifact_prior_tar_gz'], checkIfExists: true) ], + [ file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_segmentation_table'], checkIfExists: true) ], + [], + '20.0' + ] + + fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + + GATK4_FILTERMUTECTCALLS ( input, fasta, fastaidx, dict ) +} diff --git a/tests/modules/gatk4/filtermutectcalls/test.yml b/tests/modules/gatk4/filtermutectcalls/test.yml new file mode 100644 index 00000000..b17a306c --- /dev/null +++ b/tests/modules/gatk4/filtermutectcalls/test.yml @@ -0,0 +1,35 @@ +- name: gatk4 filtermutectcalls test_gatk4_filtermutectcalls_base + command: nextflow run tests/modules/gatk4/filtermutectcalls -entry test_gatk4_filtermutectcalls_base -c tests/config/nextflow.config + tags: + - gatk4 + - gatk4/filtermutectcalls + files: + - path: output/gatk4/test.filtered.vcf.gz + - path: output/gatk4/test.filtered.vcf.gz.filteringStats.tsv + md5sum: 98e1b87a52999eb8f429ef4a7877eb3f + - path: output/gatk4/test.filtered.vcf.gz.tbi + md5sum: d88d2b745c9226ddf284e3494db8b9d2 + +- name: gatk4 filtermutectcalls test_gatk4_filtermutectcalls_with_files + command: nextflow run tests/modules/gatk4/filtermutectcalls -entry test_gatk4_filtermutectcalls_with_files -c tests/config/nextflow.config + tags: + - gatk4 + - gatk4/filtermutectcalls + files: + - path: output/gatk4/test.filtered.vcf.gz + - path: output/gatk4/test.filtered.vcf.gz.filteringStats.tsv + md5sum: 98e1b87a52999eb8f429ef4a7877eb3f + - path: output/gatk4/test.filtered.vcf.gz.tbi + md5sum: d88d2b745c9226ddf284e3494db8b9d2 + +- name: gatk4 filtermutectcalls test_gatk4_filtermutectcalls_use_val + command: nextflow run tests/modules/gatk4/filtermutectcalls -entry test_gatk4_filtermutectcalls_use_val -c tests/config/nextflow.config + tags: + - gatk4 + - gatk4/filtermutectcalls + files: + - path: output/gatk4/test.filtered.vcf.gz + - path: output/gatk4/test.filtered.vcf.gz.filteringStats.tsv + md5sum: 98e1b87a52999eb8f429ef4a7877eb3f + - path: output/gatk4/test.filtered.vcf.gz.tbi + md5sum: d88d2b745c9226ddf284e3494db8b9d2