From 52b00d42863448e36a7437c944577f14ee73a285 Mon Sep 17 00:00:00 2001 From: phue Date: Wed, 17 Feb 2021 19:27:57 +0100 Subject: [PATCH] add methyldackel/mbias + tests --- .github/filters.yml | 4 ++ software/methyldackel/mbias/functions.nf | 59 ++++++++++++++++ software/methyldackel/mbias/main.nf | 44 ++++++++++++ software/methyldackel/mbias/meta.yml | 79 ++++++++++++++++++++++ tests/software/methyldackel/mbias/main.nf | 18 +++++ tests/software/methyldackel/mbias/test.yml | 8 +++ 6 files changed, 212 insertions(+) create mode 100644 software/methyldackel/mbias/functions.nf create mode 100644 software/methyldackel/mbias/main.nf create mode 100644 software/methyldackel/mbias/meta.yml create mode 100644 tests/software/methyldackel/mbias/main.nf create mode 100644 tests/software/methyldackel/mbias/test.yml diff --git a/.github/filters.yml b/.github/filters.yml index cf28883d..72862f8c 100644 --- a/.github/filters.yml +++ b/.github/filters.yml @@ -152,6 +152,10 @@ methyldackel_extract: - software/methyldackel/extract/** - tests/software/methyldackel/extract/** +methyldackel_mbias: + - software/methyldackel/mbias/** + - tests/software/methyldackel/mbias/** + minimap2_align: - software/minimap2/align/** - tests/software/minimap2/align/** diff --git a/software/methyldackel/mbias/functions.nf b/software/methyldackel/mbias/functions.nf new file mode 100644 index 00000000..d25eea86 --- /dev/null +++ b/software/methyldackel/mbias/functions.nf @@ -0,0 +1,59 @@ +/* + * ----------------------------------------------------- + * Utility functions used in nf-core DSL2 module files + * ----------------------------------------------------- + */ + +/* + * Extract name of software tool from process name using $task.process + */ +def getSoftwareName(task_process) { + return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() +} + +/* + * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules + */ +def initOptions(Map args) { + def Map options = [:] + options.args = args.args ?: '' + options.args2 = args.args2 ?: '' + options.publish_by_id = args.publish_by_id ?: false + options.publish_dir = args.publish_dir ?: '' + options.publish_files = args.publish_files + options.suffix = args.suffix ?: '' + return options +} + +/* + * Tidy up and join elements of a list to return a path string + */ +def getPathFromList(path_list) { + def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries + paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes + return paths.join('/') +} + +/* + * Function to save/publish module results + */ +def saveFiles(Map args) { + if (!args.filename.endsWith('.version.txt')) { + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + if (ioptions.publish_by_id) { + path_list.add(args.publish_id) + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" + } + } +} diff --git a/software/methyldackel/mbias/main.nf b/software/methyldackel/mbias/main.nf new file mode 100644 index 00000000..1d3b3f3b --- /dev/null +++ b/software/methyldackel/mbias/main.nf @@ -0,0 +1,44 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName } from './functions' + +params.options = [:] +def options = initOptions(params.options) + +process METHYLDACKEL_MBIAS { + tag "$meta.id" + label 'process_low' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + + conda (params.enable_conda ? "bioconda::methyldackel=0.5.0" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/methyldackel:0.5.0--hed50d52_0" + } else { + container "quay.io/biocontainers/methyldackel:0.5.0--hed50d52_0" + } + + input: + tuple val(meta), path(bam), path(bai) + path fasta + path fai + + output: + tuple val(meta), path("*.txt"), emit: txt + path "*.version.txt" , emit: version + + script: + def software = getSoftwareName(task.process) + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + """ + MethylDackel mbias \\ + $options.args \\ + $fasta \\ + $bam \\ + $prefix \\ + --txt \\ + > ${prefix}.txt + + echo \$(methyldackel --version 2>&1) | cut -f1 -d" " > ${software}.version.txt + """ +} diff --git a/software/methyldackel/mbias/meta.yml b/software/methyldackel/mbias/meta.yml new file mode 100644 index 00000000..f72a11be --- /dev/null +++ b/software/methyldackel/mbias/meta.yml @@ -0,0 +1,79 @@ +name: methyldackel_mbias +description: Generates methylation bias plots from alignments +keywords: + - methylation + - 5mC + - methylseq + - bisulphite + - methylation bias + - mbias + - qc + - bam + - cram +tools: + - methyldackel: + description: | + A (mostly) universal methylation extractor + for BS-seq experiments. + homepage: https://github.com/brentp/bwa-meth + documentation: https://github.com/brentp/bwa-meth + arxiv: arXiv:1401.1129 +params: + - outdir: + type: string + description: | + The pipeline's output directory. By default, the module will + output files into `$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 ] + - fasta: + type: file + description: Input genome fasta file + pattern: "*.{fasta,fa}" + - fai: + type: file + description: FASTA index file + pattern: "*.{fai}" + - bam: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - bai: + type: file + description: BAM/CRAM index file + pattern: "*.{bai,crai}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - txt: + type: file + description: Text file containing methylation bias + pattern: "*.{txt}" + - version: + type: file + description: File containing software version + pattern: "*.{version.txt}" +authors: + - "@phue" diff --git a/tests/software/methyldackel/mbias/main.nf b/tests/software/methyldackel/mbias/main.nf new file mode 100644 index 00000000..403082cf --- /dev/null +++ b/tests/software/methyldackel/mbias/main.nf @@ -0,0 +1,18 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { METHYLDACKEL_MBIAS } from '../../../../software/methyldackel/mbias/main.nf' addParams( options: [:] ) + +workflow test_methyldackel_mbias { + + def input = [] + def fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) + def fai = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa.fai", checkIfExists: true) + + input = [ [ id:'test', single_end:false ], // meta map + file("${launchDir}/tests/data/bam/test.paired_end_methylated.sorted.bam", checkIfExists: true), + file("${launchDir}/tests/data/bam/test.paired_end_methylated.sorted.bam.bai", checkIfExists: true) ] + + METHYLDACKEL_MBIAS ( input, fasta, fai ) +} diff --git a/tests/software/methyldackel/mbias/test.yml b/tests/software/methyldackel/mbias/test.yml new file mode 100644 index 00000000..761ef8c5 --- /dev/null +++ b/tests/software/methyldackel/mbias/test.yml @@ -0,0 +1,8 @@ +- name: Run methyldackel mbias test workflow + command: nextflow run ./tests/software/methyldackel/mbias -entry test_methyldackel_mbias -c tests/config/nextflow.config + tags: + - methyldackel + - methyldackel_mbias + files: + - path: ./output/methyldackel/test.txt + md5sum: 4a8f76da62eaa169576c8e6d509c5066