From aa32a8a72eab0c0fb4c748678916be57126a4f61 Mon Sep 17 00:00:00 2001 From: GCJMackenzie <43276267+GCJMackenzie@users.noreply.github.com> Date: Tue, 5 Oct 2021 22:52:00 +0100 Subject: [PATCH] new module: gatk4/calculatecontamination (#778) * initiated files for calculate contamination * pushing local repo to remote * created script, filled in meta yml, created tests and test yml. local checks passing, needs repo side test data * added option and tests for outputting optional segmentation file * saving for test push * versions updated, test data added * Update main.nf * fixed versions info, should report correctly now * small update to main.nf outputs formatting * Apply suggestions from code review * Update test_data.config * Apply suggestions from code review Co-authored-by: GCJMackenzie Co-authored-by: Harshil Patel --- .../gatk4/calculatecontamination/functions.nf | 78 +++++++++++++++++++ modules/gatk4/calculatecontamination/main.nf | 47 +++++++++++ modules/gatk4/calculatecontamination/meta.yml | 53 +++++++++++++ tests/config/pytest_modules.yml | 4 + tests/config/test_data.config | 2 + .../gatk4/calculatecontamination/main.nf | 38 +++++++++ .../gatk4/calculatecontamination/test.yml | 28 +++++++ 7 files changed, 250 insertions(+) create mode 100644 modules/gatk4/calculatecontamination/functions.nf create mode 100644 modules/gatk4/calculatecontamination/main.nf create mode 100644 modules/gatk4/calculatecontamination/meta.yml create mode 100644 tests/modules/gatk4/calculatecontamination/main.nf create mode 100644 tests/modules/gatk4/calculatecontamination/test.yml diff --git a/modules/gatk4/calculatecontamination/functions.nf b/modules/gatk4/calculatecontamination/functions.nf new file mode 100644 index 00000000..85628ee0 --- /dev/null +++ b/modules/gatk4/calculatecontamination/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)}/$args.filename" + } +} diff --git a/modules/gatk4/calculatecontamination/main.nf b/modules/gatk4/calculatecontamination/main.nf new file mode 100644 index 00000000..bfe9b8fd --- /dev/null +++ b/modules/gatk4/calculatecontamination/main.nf @@ -0,0 +1,47 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' + +params.options = [:] +options = initOptions(params.options) + +process GATK4_CALCULATECONTAMINATION { + tag "$meta.id" + label 'process_low' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } + + conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0" + } else { + container "quay.io/biocontainers/gatk4:4.2.0.0--0" + } + + input: + tuple val(meta), path(pileup), path(matched) + val segmentout + + output: + tuple val(meta), path('*.contamination.table') , emit: contamination + tuple val(meta), path('*.segmentation.table') , optional:true, emit: segmentation + path "versions.yml" , emit: versions + + script: + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + def matched_command = matched ? " -matched ${matched} " : '' + def segment_command = segmentout ? " -segments ${prefix}.segmentation.table" : '' + """ + gatk CalculateContamination \\ + -I $pileup \\ + $matched_command \\ + -O ${prefix}.contamination.table \\ + $segment_command \\ + $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/calculatecontamination/meta.yml b/modules/gatk4/calculatecontamination/meta.yml new file mode 100644 index 00000000..0d1b9b85 --- /dev/null +++ b/modules/gatk4/calculatecontamination/meta.yml @@ -0,0 +1,53 @@ +name: gatk4_calculatecontamination +description: | + Calculates the fraction of reads from cross-sample contamination based on summary tables from getpileupsummaries. Output to be used with filtermutectcalls. +keywords: + - gatk4 + - calculatecontamination + - cross-samplecontamination + - getpileupsummaries + - filtermutectcalls +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' ] + - pileup: + type: file + description: File containing the pileups summary table of a tumor sample to be used to calculate contamination. + pattern: "*.pileups.table" + - matched: + type: file + description: File containing the pileups summary table of a normal sample that matches with the tumor sample specified in pileup argument. This is an optional input. + pattern: "*.pileups.table" + - segmentout: + type: boolean + description: specifies whether to output the segmentation table. + +output: + - contamination: + type: file + description: File containing the contamination table. + pattern: "*.contamination.table" + - segmentation: + type: file + description: optional output table containing segmentation of tumor minor allele fractions. + pattern: "*.segmentation.table" + - 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 ec3e8ed4..340ea28d 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -386,6 +386,10 @@ gatk4/bedtointervallist: - modules/gatk4/bedtointervallist/** - tests/modules/gatk4/bedtointervallist/** +gatk4/calculatecontamination: + - modules/gatk4/calculatecontamination/** + - tests/modules/gatk4/calculatecontamination/** + gatk4/createsequencedictionary: - modules/gatk4/createsequencedictionary/** - tests/modules/gatk4/createsequencedictionary/** diff --git a/tests/config/test_data.config b/tests/config/test_data.config index 8d5ecd92..8fcc3d0b 100644 --- a/tests/config/test_data.config +++ b/tests/config/test_data.config @@ -153,6 +153,8 @@ params { test_baserecalibrator_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table" test2_baserecalibrator_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.baserecalibrator.table" + test_pileups_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.pileups.table" + test2_pileups_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.pileups.table" test_genome_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf" test_genome_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz" diff --git a/tests/modules/gatk4/calculatecontamination/main.nf b/tests/modules/gatk4/calculatecontamination/main.nf new file mode 100644 index 00000000..f93f66fb --- /dev/null +++ b/tests/modules/gatk4/calculatecontamination/main.nf @@ -0,0 +1,38 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { GATK4_CALCULATECONTAMINATION } from '../../../../modules/gatk4/calculatecontamination/main.nf' addParams( options: [:] ) + +workflow test_gatk4_calculatecontamination_tumor_only { + + input = [ [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test2_pileups_table'], checkIfExists: true), + [] ] + + segmentout = false + + GATK4_CALCULATECONTAMINATION ( input, segmentout ) +} + +workflow test_gatk4_calculatecontamination_matched_pair { + + input = [ [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test2_pileups_table'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_pileups_table'], checkIfExists: true) ] + + segmentout = false + + GATK4_CALCULATECONTAMINATION ( input, segmentout ) +} + +workflow test_gatk4_calculatecontamination_segmentation { + + input = [ [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test2_pileups_table'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_pileups_table'], checkIfExists: true) ] + + segmentout = true + + GATK4_CALCULATECONTAMINATION ( input, segmentout ) +} diff --git a/tests/modules/gatk4/calculatecontamination/test.yml b/tests/modules/gatk4/calculatecontamination/test.yml new file mode 100644 index 00000000..8736bc32 --- /dev/null +++ b/tests/modules/gatk4/calculatecontamination/test.yml @@ -0,0 +1,28 @@ +- name: gatk4 calculatecontamination test_gatk4_calculatecontamination_tumor_only + command: nextflow run tests/modules/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_tumor_only -c tests/config/nextflow.config + tags: + - gatk4/calculatecontamination + - gatk4 + files: + - path: output/gatk4/test.contamination.table + md5sum: ff348a26dd09404239a7ed0da7d98874 + +- name: gatk4 calculatecontamination test_gatk4_calculatecontamination_matched_pair + command: nextflow run tests/modules/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_matched_pair -c tests/config/nextflow.config + tags: + - gatk4/calculatecontamination + - gatk4 + files: + - path: output/gatk4/test.contamination.table + md5sum: ff348a26dd09404239a7ed0da7d98874 + +- name: gatk4 calculatecontamination test_gatk4_calculatecontamination_segmentation + command: nextflow run tests/modules/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_segmentation -c tests/config/nextflow.config + tags: + - gatk4/calculatecontamination + - gatk4 + files: + - path: output/gatk4/test.contamination.table + md5sum: ff348a26dd09404239a7ed0da7d98874 + - path: output/gatk4/test.segmentation.table + md5sum: 478cb4f69ec001944b9cd0e7e4de01ef