From 035443b6e092321b65574ab09620c731ed6975aa Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Tue, 23 Feb 2021 19:05:26 +0100 Subject: [PATCH] Add bcftools-mpileup module --- software/bcftools/mpileup/functions.nf | 61 +++++++++++++++++++++++ software/bcftools/mpileup/main.nf | 46 +++++++++++++++++ software/bcftools/mpileup/meta.yml | 69 ++++++++++++++++++++++++++ 3 files changed, 176 insertions(+) create mode 100644 software/bcftools/mpileup/functions.nf create mode 100644 software/bcftools/mpileup/main.nf create mode 100644 software/bcftools/mpileup/meta.yml diff --git a/software/bcftools/mpileup/functions.nf b/software/bcftools/mpileup/functions.nf new file mode 100644 index 00000000..779feec6 --- /dev/null +++ b/software/bcftools/mpileup/functions.nf @@ -0,0 +1,61 @@ + +/* + * ----------------------------------------------------- + * Utility functions used in nf-core DSL2 module files + * ----------------------------------------------------- + */ + +/* + * Extract name of software tool from process name using $task.process + */ +def getSoftwareName(task_process) { + return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() +} + +/* + * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules + */ +def initOptions(Map args) { + def Map options = [:] + options.args = args.args ?: '' + options.args2 = args.args2 ?: '' + options.args3 = args.args3 ?: '' + options.publish_by_id = args.publish_by_id ?: false + options.publish_dir = args.publish_dir ?: '' + options.publish_files = args.publish_files + options.suffix = args.suffix ?: '' + return options +} + +/* + * Tidy up and join elements of a list to return a path string + */ +def getPathFromList(path_list) { + def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries + paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", '') } // Trim whitespace and trailing slashes + return paths.join('/') +} + +/* + * Function to save/publish module results + */ +def saveFiles(Map args) { + if (!args.filename.endsWith('.version.txt')) { + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + if (ioptions.publish_by_id) { + path_list.add(args.publish_id) + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" + } + } +} diff --git a/software/bcftools/mpileup/main.nf b/software/bcftools/mpileup/main.nf new file mode 100644 index 00000000..22f32f90 --- /dev/null +++ b/software/bcftools/mpileup/main.nf @@ -0,0 +1,46 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName } from './functions' + +params.options = [:] +def options = initOptions(params.options) + +process BCFTOOLS_MPILEUP { + tag "$meta.id" + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + + conda (params.enable_conda ? "bioconda::bcftools=1.11" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0" + } else { + container "quay.io/biocontainers/bcftools:1.11--h7c999a4_0" + } + + input: + tuple val(meta), path(bam) + path fasta + + output: + tuple val(meta), path("*.gz") , emit: vcf + tuple val(meta), path("*.tbi") , emit: tbi + tuple val(meta), path("*stats.txt"), emit: stats + path "*.version.txt" , emit: version + + script: + def software = getSoftwareName(task.process) + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + """ + echo "${meta.id}" > sample_name.list + bcftools mpileup \\ + --fasta-ref $fasta \\ + $options.args \\ + $bam \\ + | bcftools call --output-type v $options.args2 \\ + | bcftools reheader --samples sample_name.list \\ + | bcftools view --output-file ${prefix}.vcf.gz --output-type z $options.args3 + tabix -p vcf -f ${prefix}.vcf.gz + bcftools stats ${prefix}.vcf.gz > ${prefix}.bcftools_stats.txt + echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt + """ +} diff --git a/software/bcftools/mpileup/meta.yml b/software/bcftools/mpileup/meta.yml new file mode 100644 index 00000000..4f137d5f --- /dev/null +++ b/software/bcftools/mpileup/meta.yml @@ -0,0 +1,69 @@ +name: bcftools_mpileup +description: Compresses VCF files +keywords: + - variant calling + - mpileup + - VCF +tools: + - consensus: + description: | + Generates genotype likelihoods at each genomic position with coverage. + homepage: http://samtools.github.io/bcftools/bcftools.html + documentation: http://www.htslib.org/doc/bcftools.html + doi: 10.1093/bioinformatics/btp352 +params: + - outdir: + type: string + description: | + The pipeline's output directory. By default, the module will + output files into `$params.outdir/` + - publish_dir_mode: + type: string + description: | + Value for the Nextflow `publishDir` mode parameter. + Available: symlink, rellink, link, copy, copyNoFollow, move. + - enable_conda: + type: boolean + description: | + Run the module with Conda using the software specified + via the `conda` directive + - singularity_pull_docker_container: + type: boolean + description: | + Instead of directly downloading Singularity images for use with Singularity, + force the workflow to pull and convert Docker containers instead. +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Input BAM file + pattern: "*.{bam}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: FASTA reference consensus file + pattern: "*.{fasta,fa}" + - tbi: + type: file + description: tabix index file + pattern: "*.{tbi}" + - stats: + type: file + description: Text output file containing stats + pattern: "*{stats.txt}" + - version: + type: file + description: File containing software version + pattern: "*.{version.txt}" +authors: + - "@joseespinosa" + - "@drpatelh"