diff --git a/modules/bcftools/concat/functions.nf b/modules/bcftools/concat/functions.nf new file mode 100644 index 00000000..da9da093 --- /dev/null +++ b/modules/bcftools/concat/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)}/$args.filename" + } + } +} diff --git a/modules/bcftools/concat/main.nf b/modules/bcftools/concat/main.nf new file mode 100644 index 00000000..0266f4f0 --- /dev/null +++ b/modules/bcftools/concat/main.nf @@ -0,0 +1,40 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName } from './functions' + +params.options = [:] +options = initOptions(params.options) + +process BCFTOOLS_CONCAT { + tag "$meta.id" + label 'process_medium' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } + + conda (params.enable_conda ? "bioconda::bcftools=1.11" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0" + } else { + container "quay.io/biocontainers/bcftools:1.11--h7c999a4_0" + } + + input: + tuple val(meta), path(vcfs) + + output: + tuple val(meta), path("*.gz"), emit: vcf + path "*.version.txt" , emit: version + + script: + def software = getSoftwareName(task.process) + prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + """ + bcftools concat \\ + --output ${prefix}.vcf.gz \\ + $options.args \\ + --threads $task.cpus \\ + ${vcfs} + + echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt + """ +} diff --git a/modules/bcftools/concat/meta.yml b/modules/bcftools/concat/meta.yml new file mode 100644 index 00000000..566e6dba --- /dev/null +++ b/modules/bcftools/concat/meta.yml @@ -0,0 +1,42 @@ +name: bcftools_concat +description: Concatenate VCF files +keywords: + - variant calling + - concat + - bcftools + - VCF + +tools: + - concat: + description: | + Concatenate VCF files. + homepage: http://samtools.github.io/bcftools/bcftools.html + documentation: http://www.htslib.org/doc/bcftools.html + doi: 10.1093/bioinformatics/btp352 +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcfs: + type: files + description: | + List containing 2 or more vcf files + e.g. [ 'file1.vcf', 'file2.vcf' ] +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF concatenated output file + pattern: "*.{vcf.gz}" + - version: + type: file + description: File containing software version + pattern: "*.{version.txt}" +authors: + - "@abhi18av" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 39b267c7..dc9933d9 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -30,6 +30,10 @@ bbmap/bbduk: - modules/bbmap/bbduk/** - tests/modules/bbmap/bbduk/** +bcftools/concat: + - modules/bcftools/concat/** + - tests/modules/bcftools/concat/** + bcftools/consensus: - modules/bcftools/consensus/** - tests/modules/bcftools/consensus/** diff --git a/tests/modules/bcftools/concat/main.nf b/tests/modules/bcftools/concat/main.nf new file mode 100644 index 00000000..8869a3d7 --- /dev/null +++ b/tests/modules/bcftools/concat/main.nf @@ -0,0 +1,16 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { BCFTOOLS_CONCAT } from '../../../../modules/bcftools/concat/main.nf' addParams( options: ['args': '--no-version'] ) + +workflow test_bcftools_concat { + + input = [ [ id:'test3' ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) ] + ] + + + BCFTOOLS_CONCAT ( input ) +} diff --git a/tests/modules/bcftools/concat/test.yml b/tests/modules/bcftools/concat/test.yml new file mode 100644 index 00000000..413fe798 --- /dev/null +++ b/tests/modules/bcftools/concat/test.yml @@ -0,0 +1,8 @@ +- name: bcftools concat test_bcftools_concat + command: nextflow run tests/modules/bcftools/concat -entry test_bcftools_concat -c tests/config/nextflow.config + tags: + - bcftools/concat + - bcftools + files: + - path: output/bcftools/test3.vcf.gz + md5sum: c400c7458524d889e0967b06ed72534f