From a813e2e3a6b45585603c6f09d946d9bbbab914f6 Mon Sep 17 00:00:00 2001 From: Johnathan D <28043284+bjohnnyd@users.noreply.github.com> Date: Fri, 23 Jul 2021 22:24:19 +0100 Subject: [PATCH] Add bcftools reheader (#585) (#608) * local tests and linting passing (#585) * fix: picard filtersamreads input (#610) * Move readlist into same input channel as bam * Update test reflecting input restructuring * Update tests/modules/picard/filtersamreads/main.nf Co-authored-by: Harshil Patel * fix test Co-authored-by: Harshil Patel * Added module arriba (#611) * Updated the version of STAR in align and genomegenerate modules * Changes in test.yml * Changes in test.yml * Added module arriba * Changes in test configs * Added module Arriba for fusion detection * Fixed review comments * Added an output option for discarded fusions * Resolved some conflits * conflicts * Apply suggestions from code review Co-authored-by: Harshil Patel * added test for new header * enhance module fastp: add `save_merged` (#598) (#614) * enhance module fastp: add `save_merged` (#598) * removed md5sum checks from log and json * Apply suggestions from code review Co-authored-by: James A. Fellows Yates Co-authored-by: Harshil Patel Co-authored-by: praveenraj2018 <43108054+praveenraj2018@users.noreply.github.com> --- modules/bcftools/reheader/functions.nf | 68 ++++++++++++++++++++++++ modules/bcftools/reheader/main.nf | 47 ++++++++++++++++ modules/bcftools/reheader/meta.yml | 51 ++++++++++++++++++ tests/config/pytest_modules.yml | 4 ++ tests/modules/bcftools/reheader/main.nf | 40 ++++++++++++++ tests/modules/bcftools/reheader/test.yml | 26 +++++++++ 6 files changed, 236 insertions(+) create mode 100644 modules/bcftools/reheader/functions.nf create mode 100644 modules/bcftools/reheader/main.nf create mode 100644 modules/bcftools/reheader/meta.yml create mode 100644 tests/modules/bcftools/reheader/main.nf create mode 100644 tests/modules/bcftools/reheader/test.yml diff --git a/modules/bcftools/reheader/functions.nf b/modules/bcftools/reheader/functions.nf new file mode 100644 index 00000000..da9da093 --- /dev/null +++ b/modules/bcftools/reheader/functions.nf @@ -0,0 +1,68 @@ +// +// Utility functions used in nf-core DSL2 module files +// + +// +// Extract name of software tool from process name using $task.process +// +def getSoftwareName(task_process) { + return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() +} + +// +// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules +// +def initOptions(Map args) { + def Map options = [:] + options.args = args.args ?: '' + options.args2 = args.args2 ?: '' + options.args3 = args.args3 ?: '' + options.publish_by_meta = args.publish_by_meta ?: [] + options.publish_dir = args.publish_dir ?: '' + options.publish_files = args.publish_files + options.suffix = args.suffix ?: '' + return options +} + +// +// Tidy up and join elements of a list to return a path string +// +def getPathFromList(path_list) { + def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries + paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes + return paths.join('/') +} + +// +// Function to save/publish module results +// +def saveFiles(Map args) { + if (!args.filename.endsWith('.version.txt')) { + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${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)}/$args.filename" + } + } +} diff --git a/modules/bcftools/reheader/main.nf b/modules/bcftools/reheader/main.nf new file mode 100644 index 00000000..53b00411 --- /dev/null +++ b/modules/bcftools/reheader/main.nf @@ -0,0 +1,47 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName } from './functions' + +params.options = [:] +options = initOptions(params.options) + +process BCFTOOLS_REHEADER { + tag "$meta.id" + label 'process_low' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } + + conda (params.enable_conda ? "bioconda::bcftools=1.13" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0" + } else { + container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0" + } + + input: + tuple val(meta), path(vcf) + path fai + path header + + output: + tuple val(meta), path("*.vcf.gz"), emit: vcf + path "*.version.txt" , emit: version + + script: + def software = getSoftwareName(task.process) + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + def update_sequences = fai ? "-f $fai" : "" + def new_header = header ? "-h $header" : "" + """ + bcftools \\ + reheader \\ + $update_sequences \\ + $new_header \\ + $options.args \\ + --threads $task.cpus \\ + -o ${prefix}.vcf.gz \\ + $vcf + + echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt + """ +} diff --git a/modules/bcftools/reheader/meta.yml b/modules/bcftools/reheader/meta.yml new file mode 100644 index 00000000..1b9c1a8b --- /dev/null +++ b/modules/bcftools/reheader/meta.yml @@ -0,0 +1,51 @@ +name: bcftools_reheader +description: Reheader a VCF file +keywords: + - reheader + - vcf + - update header +tools: + - reheader: + description: | + Modify header of VCF/BCF files, change sample names. + homepage: http://samtools.github.io/bcftools/bcftools.html + documentation: http://samtools.github.io/bcftools/bcftools.html#reheader + doi: 10.1093/gigascience/giab008 + licence: ['GPL'] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF/BCF file + pattern: "*.{vcf.gz,vcf,bcf}" + - fai: + type: file + description: Fasta index to update header sequences with + pattern: "*.{fai}" + - header: + type: file + description: New header to add to the VCF + pattern: "*.{header.txt}" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - version: + type: file + description: File containing software version + pattern: "*.{version.txt}" + - vcf: + type: file + description: VCF with updated header + pattern: "*.{vcf.gz}" + +authors: + - "@bjohnnyd" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 429b0ebd..69e39d91 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -50,6 +50,10 @@ bcftools/mpileup: - modules/bcftools/mpileup/** - tests/modules/bcftools/mpileup/** +bcftools/reheader: + - modules/bcftools/reheader/** + - tests/modules/bcftools/reheader/** + bcftools/stats: - modules/bcftools/stats/** - tests/modules/bcftools/stats/** diff --git a/tests/modules/bcftools/reheader/main.nf b/tests/modules/bcftools/reheader/main.nf new file mode 100644 index 00000000..40863331 --- /dev/null +++ b/tests/modules/bcftools/reheader/main.nf @@ -0,0 +1,40 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { BCFTOOLS_REHEADER } from '../../../../modules/bcftools/reheader/main.nf' addParams( options: [suffix: '.updated'] ) + +workflow test_bcftools_reheader_update_sequences { + + input = [ + [ id:'test', single_end:false ], + file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) + ] + fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + header = [] + BCFTOOLS_REHEADER ( input, fai, header ) +} + +workflow test_bcftools_reheader_new_header { + + input = [ + [ id:'test', single_end:false ], + file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) + ] + fai = [] + header = file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) + + BCFTOOLS_REHEADER ( input, fai, header ) +} + +workflow test_bcftools_reheader_new_header_update_sequences { + + input = [ + [ id:'test', single_end:false ], + file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) + ] + fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + header = file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) + + BCFTOOLS_REHEADER ( input, fai, header ) +} diff --git a/tests/modules/bcftools/reheader/test.yml b/tests/modules/bcftools/reheader/test.yml new file mode 100644 index 00000000..78337206 --- /dev/null +++ b/tests/modules/bcftools/reheader/test.yml @@ -0,0 +1,26 @@ +- name: bcftools reheader test_bcftools_reheader_update_sequences + command: nextflow run tests/modules/bcftools/reheader -entry test_bcftools_reheader_update_sequences -c tests/config/nextflow.config + tags: + - bcftools/reheader + - bcftools + files: + - path: output/bcftools/test.updated.vcf.gz + md5sum: 9e29f28038bfce77ee00022627209ed6 + +- name: bcftools reheader test_bcftools_reheader_new_header + command: nextflow run tests/modules/bcftools/reheader -entry test_bcftools_reheader_new_header -c tests/config/nextflow.config + tags: + - bcftools/reheader + - bcftools + files: + - path: output/bcftools/test.updated.vcf.gz + md5sum: f7f536d889bbf5be40243252c394ee1f + +- name: bcftools reheader test_bcftools_reheader_new_header_update_sequences + command: nextflow run tests/modules/bcftools/reheader -entry test_bcftools_reheader_new_header_update_sequences -c tests/config/nextflow.config + tags: + - bcftools/reheader + - bcftools + files: + - path: output/bcftools/test.updated.vcf.gz + md5sum: 9e29f28038bfce77ee00022627209ed6