From 3c4d9466f4c2db729e62fc8560b22c5ac61ccd25 Mon Sep 17 00:00:00 2001 From: Kevin Menden Date: Wed, 17 Mar 2021 12:54:15 +0100 Subject: [PATCH] Adding minia for viralrecon (#267) * initial 'modules create' of minia * fixed tests * finished meta.yml * fixed filters.yml * resolved issues in pytest_software.yml * add newline * Update software/minia/main.nf Co-authored-by: Harshil Patel --- software/minia/functions.nf | 59 ++++++++++++++++++++++++++++ software/minia/main.nf | 41 +++++++++++++++++++ software/minia/meta.yml | 67 ++++++++++++++++++++++++++++++++ tests/config/pytest_software.yml | 16 ++++---- tests/software/minia/main.nf | 15 +++++++ tests/software/minia/test.yml | 8 ++++ 6 files changed, 198 insertions(+), 8 deletions(-) create mode 100644 software/minia/functions.nf create mode 100644 software/minia/main.nf create mode 100644 software/minia/meta.yml create mode 100644 tests/software/minia/main.nf create mode 100644 tests/software/minia/test.yml diff --git a/software/minia/functions.nf b/software/minia/functions.nf new file mode 100644 index 00000000..d25eea86 --- /dev/null +++ b/software/minia/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)}/$args.filename" + } + } +} diff --git a/software/minia/main.nf b/software/minia/main.nf new file mode 100644 index 00000000..b2b4df8f --- /dev/null +++ b/software/minia/main.nf @@ -0,0 +1,41 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName } from './functions' + +params.options = [:] +def options = initOptions(params.options) +process MINIA { + tag "$meta.id" + label 'process_high' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + + conda (params.enable_conda ? "bioconda::minia=3.2.4" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/minia:3.2.4--he513fc3_0" + } else { + container "quay.io/biocontainers/minia:3.2.4--he513fc3_0" + } + + input: + tuple val(meta), path(reads) + + output: + tuple val(meta), path('*.contigs.fa'), emit: contigs + tuple val(meta), path('*.unitigs.fa'), emit: unitigs + tuple val(meta), path('*.h5') , emit: h5 + path '*.version.txt' , emit: version + + script: + def software = getSoftwareName(task.process) + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + """ + echo "${reads.join("\n")}" > input_files.txt + minia \\ + $options.args \\ + -nb-cores $task.cpus \\ + -in input_files.txt \\ + -out $prefix + echo \$(minia --version 2>&1) | sed 's/^.*Minia version //; s/ .*\$//' > ${software}.version.txt + """ +} diff --git a/software/minia/meta.yml b/software/minia/meta.yml new file mode 100644 index 00000000..17f0eb7f --- /dev/null +++ b/software/minia/meta.yml @@ -0,0 +1,67 @@ +name: minia +description: Minia is a short-read assembler based on a de Bruijn graph +keywords: + - assembly +tools: + - minia: + description: | + Minia is a short-read assembler based on a de Bruijn graph, capable of assembling + a human genome on a desktop computer in a day. The output of Minia is a set of contigs. + homepage: https://github.com/GATB/minia + documentation: https://github.com/GATB/minia +params: + - outdir: + type: string + description: | + The pipeline's output directory. By default, the module will + output files into `$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 ] + - reads: + type: file + description: Input reads in FastQ format + pattern: "*.{fastq.gz, fastq}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - contigs: + type: file + description: The assembled contigs + pattern: "*.contigs.fa" + - unitigs: + type: file + description: The assembled unitigs + pattern: "*.unitigs.fa" + - h5: + type: file + description: Minia output h5 file + pattern: "*{.h5}" + - version: + type: file + description: File containing software version + pattern: "*.{version.txt}" +authors: + - "@drpatelh" + - "@kevinmenden" diff --git a/tests/config/pytest_software.yml b/tests/config/pytest_software.yml index eece533c..fea94247 100644 --- a/tests/config/pytest_software.yml +++ b/tests/config/pytest_software.yml @@ -66,10 +66,6 @@ bismark_genome_preparation: - software/bismark/genome_preparation/** - tests/software/bismark/genome_preparation/** -blast_makeblastdb: - - software/blast/makeblastdb/** - - tests/software/blast/makeblastdb/** - blast_blastn: - software/blast/blastn/** - tests/software/blast/blastn/** @@ -192,6 +188,10 @@ methyldackel_mbias: - software/methyldackel/mbias/** - tests/software/methyldackel/mbias/** +minia: + - software/minia/** + - tests/software/minia/** + minimap2_align: - software/minimap2/align/** - tests/software/minimap2/align/** @@ -313,14 +313,14 @@ trimgalore: - software/trimgalore/** - tests/software/trimgalore/** -untar: - - software/untar/** - - tests/software/untar/** - ucsc_bedgraphtobigwig: - software/ucsc/bedgraphtobigwig/** - tests/software/ucsc/bedgraphtobigwig/** +untar: + - software/untar/** + - tests/software/untar/** + gatk4_variantfiltration: - software/gatk4/variantfiltration/** - tests/software/gatk4/variantfiltration/** diff --git a/tests/software/minia/main.nf b/tests/software/minia/main.nf new file mode 100644 index 00000000..ae1f487b --- /dev/null +++ b/tests/software/minia/main.nf @@ -0,0 +1,15 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { MINIA } from '../../../software/minia/main.nf' addParams( options: [:] ) + +workflow test_minia { + + def input = [] + input = [ [ id:'test' ], // meta map + [file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true), + file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_2.fastq.gz", checkIfExists: true)] ] + + MINIA ( input ) +} diff --git a/tests/software/minia/test.yml b/tests/software/minia/test.yml new file mode 100644 index 00000000..eed0b640 --- /dev/null +++ b/tests/software/minia/test.yml @@ -0,0 +1,8 @@ +- name: Run tests for minia - test_minia + command: nextflow run tests/software/minia -entry test_minia -c tests/config/nextflow.config + tags: + - minia + files: + - path: output/minia/test.h5 + - path: output/minia/test.contigs.fa + - path: output/minia/test.unitigs.fa