From f479d4fb8d634b5ac5bd1c879917dc285abc076d Mon Sep 17 00:00:00 2001 From: GCJMackenzie <43276267+GCJMackenzie@users.noreply.github.com> Date: Thu, 7 Oct 2021 13:55:06 +0100 Subject: [PATCH] Learnreadorientationmodel (#794) * files for learnreadorientationmodel initialised for first commit * finished scripts and yml files. test working locally but needs an f1r2 test data on nf-core before it can be submitted * updated test data location * versions file updated, test data added * updated versions file, edited test file * small formatting update to main.nf * Update main.nf * Update test_data.config * updated tests main.nf * Update test_data.config * Apply suggestions from code review * Update modules/gatk4/learnreadorientationmodel/main.nf * Update modules/gatk4/learnreadorientationmodel/meta.yml * fixed tests failing Co-authored-by: GCJMackenzie Co-authored-by: Harshil Patel --- .../learnreadorientationmodel/functions.nf | 78 +++++++++++++++++++ .../gatk4/learnreadorientationmodel/main.nf | 44 +++++++++++ .../gatk4/learnreadorientationmodel/meta.yml | 41 ++++++++++ tests/config/pytest_modules.yml | 4 + tests/config/test_data.config | 8 ++ .../gatk4/learnreadorientationmodel/main.nf | 13 ++++ .../gatk4/learnreadorientationmodel/test.yml | 7 ++ 7 files changed, 195 insertions(+) create mode 100644 modules/gatk4/learnreadorientationmodel/functions.nf create mode 100644 modules/gatk4/learnreadorientationmodel/main.nf create mode 100644 modules/gatk4/learnreadorientationmodel/meta.yml create mode 100644 tests/modules/gatk4/learnreadorientationmodel/main.nf create mode 100644 tests/modules/gatk4/learnreadorientationmodel/test.yml diff --git a/modules/gatk4/learnreadorientationmodel/functions.nf b/modules/gatk4/learnreadorientationmodel/functions.nf new file mode 100644 index 00000000..85628ee0 --- /dev/null +++ b/modules/gatk4/learnreadorientationmodel/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)}/$args.filename" + } +} diff --git a/modules/gatk4/learnreadorientationmodel/main.nf b/modules/gatk4/learnreadorientationmodel/main.nf new file mode 100644 index 00000000..0a499def --- /dev/null +++ b/modules/gatk4/learnreadorientationmodel/main.nf @@ -0,0 +1,44 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' + +params.options = [:] +options = initOptions(params.options) + +process GATK4_LEARNREADORIENTATIONMODEL { + tag "$meta.id" + label 'process_low' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } + + conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0" + } else { + container "quay.io/biocontainers/gatk4:4.2.0.0--0" + } + + input: + tuple val(meta), path(f1r2) + + output: + tuple val(meta), path("*.tar.gz"), emit: artifactprior + path "versions.yml" , emit: versions + + script: + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + def inputs_list = [] + f1r2.each() { a -> inputs_list.add(" -I " + a) } + """ + gatk \\ + LearnReadOrientationModel \\ + ${inputs_list.join(' ')} \\ + -O ${prefix}.tar.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/learnreadorientationmodel/meta.yml b/modules/gatk4/learnreadorientationmodel/meta.yml new file mode 100644 index 00000000..c15b48cb --- /dev/null +++ b/modules/gatk4/learnreadorientationmodel/meta.yml @@ -0,0 +1,41 @@ +name: gatk4_learnreadorientationmodel +description: | + Uses f1r2 counts collected during mutect2 to Learn the prior probability of read orientation artifacts +keywords: + - gatk4 + - learnreadorientationmodel + - readorientationartifacts + - mutect2 +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' ] + - f1r2: + type: list + description: list of f1r2 files to be used as input. + pattern: "*.f1r2.tar.gz" + +output: + - artifactprior: + type: file + description: file containing artifact-priors to be used by filtermutectcalls + pattern: "*.tar.gz" + - 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 6f0e491f..45a4d62c 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -410,6 +410,10 @@ gatk4/intervallisttools: - modules/gatk4/intervallisttools/** - tests/modules/gatk4/intervallisttools/** +gatk4/learnreadorientationmodel: + - modules/gatk4/learnreadorientationmodel/** + - tests/modules/gatk4/learnreadorientationmodel/** + gatk4/markduplicates: - modules/gatk4/markduplicates/** - tests/modules/gatk4/markduplicates/** diff --git a/tests/config/test_data.config b/tests/config/test_data.config index 8fcc3d0b..30e6f1ea 100644 --- a/tests/config/test_data.config +++ b/tests/config/test_data.config @@ -155,6 +155,14 @@ params { 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_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 = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.stats" + test_test2_paired_mutect2_calls_f1r2_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.f1r2.tar.gz" + test_test2_paired_mutect2_calls_artifact_prior_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired_mutect2_calls.artifact-prior.tar.gz" + test_test2_paired_segmentation_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired.segmentation.table" + test_test2_paired_contamination_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired.contamination.table" test_genome_vcf = "${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/learnreadorientationmodel/main.nf b/tests/modules/gatk4/learnreadorientationmodel/main.nf new file mode 100644 index 00000000..1a71873e --- /dev/null +++ b/tests/modules/gatk4/learnreadorientationmodel/main.nf @@ -0,0 +1,13 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { GATK4_LEARNREADORIENTATIONMODEL } from '../../../../modules/gatk4/learnreadorientationmodel/main.nf' addParams( options: [suffix:'.artifact-prior'] ) + +workflow test_gatk4_learnreadorientationmodel { + + input = [ [ id:'test' ], // meta map + [file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_f1r2_tar_gz'], checkIfExists: true)] ] + + GATK4_LEARNREADORIENTATIONMODEL ( input ) +} diff --git a/tests/modules/gatk4/learnreadorientationmodel/test.yml b/tests/modules/gatk4/learnreadorientationmodel/test.yml new file mode 100644 index 00000000..6e999fa6 --- /dev/null +++ b/tests/modules/gatk4/learnreadorientationmodel/test.yml @@ -0,0 +1,7 @@ +- name: gatk4 learnreadorientationmodel test_gatk4_learnreadorientationmodel + command: nextflow run tests/modules/gatk4/learnreadorientationmodel -entry test_gatk4_learnreadorientationmodel -c tests/config/nextflow.config + tags: + - gatk4 + - gatk4/learnreadorientationmodel + files: + - path: output/gatk4/test.artifact-prior.tar.gz