From d1794d19346dcbc0812e97c1e7b5516d19b88d12 Mon Sep 17 00:00:00 2001 From: Mei Wu Date: Wed, 13 Oct 2021 12:59:35 +0200 Subject: [PATCH] Add TIDDIT cov (#822) * added template for tiddit/cov * test finished * quick fix to meta info * Apply suggestions from code review Co-authored-by: James A. Fellows Yates * applying suggestions Co-authored-by: James A. Fellows Yates Co-authored-by: James A. Fellows Yates --- modules/tiddit/cov/functions.nf | 78 +++++++++++++++++++++++++++++++ modules/tiddit/cov/main.nf | 49 +++++++++++++++++++ modules/tiddit/cov/meta.yml | 52 +++++++++++++++++++++ tests/config/pytest_modules.yml | 4 ++ tests/modules/tiddit/cov/main.nf | 23 +++++++++ tests/modules/tiddit/cov/test.yml | 17 +++++++ 6 files changed, 223 insertions(+) create mode 100644 modules/tiddit/cov/functions.nf create mode 100644 modules/tiddit/cov/main.nf create mode 100644 modules/tiddit/cov/meta.yml create mode 100644 tests/modules/tiddit/cov/main.nf create mode 100644 tests/modules/tiddit/cov/test.yml diff --git a/modules/tiddit/cov/functions.nf b/modules/tiddit/cov/functions.nf new file mode 100644 index 00000000..85628ee0 --- /dev/null +++ b/modules/tiddit/cov/functions.nf @@ -0,0 +1,78 @@ +// +// 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() +} + +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + +// +// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules +// +def initOptions(Map args) { + def Map options = [:] + options.args = args.args ?: '' + options.args2 = args.args2 ?: '' + options.args3 = args.args3 ?: '' + options.publish_by_meta = args.publish_by_meta ?: [] + options.publish_dir = args.publish_dir ?: '' + options.publish_files = args.publish_files + options.suffix = args.suffix ?: '' + return options +} + +// +// Tidy up and join elements of a list to return a path string +// +def getPathFromList(path_list) { + def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries + paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes + return paths.join('/') +} + +// +// Function to save/publish module results +// +def saveFiles(Map args) { + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${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)}/$args.filename" + } +} diff --git a/modules/tiddit/cov/main.nf b/modules/tiddit/cov/main.nf new file mode 100644 index 00000000..a3a8a171 --- /dev/null +++ b/modules/tiddit/cov/main.nf @@ -0,0 +1,49 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' + +params.options = [:] +options = initOptions(params.options) + +process TIDDIT_COV { + tag "$meta.id" + label 'process_low' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } + + conda (params.enable_conda ? "bioconda::tiddit=2.12.1" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/tiddit:2.12.1--py38h1773678_0" + } else { + container "quay.io/biocontainers/tiddit:2.12.1--py38h1773678_0" + } + + input: + tuple val(meta), path(bam) + path fasta + + output: + tuple val(meta), path("*.tab"), optional: true, emit: cov + tuple val(meta), path("*.wig"), optional: true, emit: wig + + path "versions.yml" , emit: versions + + script: + def software = getSoftwareName(task.process) + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + + def reference = fasta ? "--ref $fasta" : "" + """ + tiddit \\ + --cov \\ + -o $prefix \\ + $options.args \\ + --bam $bam \\ + $reference + + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//') + END_VERSIONS + """ +} diff --git a/modules/tiddit/cov/meta.yml b/modules/tiddit/cov/meta.yml new file mode 100644 index 00000000..d925b783 --- /dev/null +++ b/modules/tiddit/cov/meta.yml @@ -0,0 +1,52 @@ +name: tiddit_cov +description: Computes the coverage of different regions from the bam file. +keywords: + - coverage + - bam + - statistics + - chromosomal rearrangements +tools: + - tiddit: + description: TIDDIT - structural variant calling. + homepage: https://github.com/SciLifeLab/TIDDIT + documentation: https://github.com/SciLifeLab/TIDDIT/blob/master/README.md + doi: "10.12688/f1000research.11168.1" + licence: ["GPL v3"] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - fasta: + type: file + description: | + Reference genome file. Only needed when passing in CRAM instead of BAM. + If not using CRAM, please pass an empty file instead. + pattern: "*.fasta" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - cov: + type: file + description: The coverage of different regions. Optional. + pattern: "*.tab" + - wig: + type: file + description: The coverage of different regions in WIG format. Optional. + pattern: "*.wig" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@projectoriented" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 747efd3a..6bc07f92 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -1039,6 +1039,10 @@ tabix/tabix: - modules/tabix/tabix/** - tests/modules/tabix/tabix/** +tiddit/cov: + - modules/tiddit/cov/** + - tests/modules/tiddit/cov/** + tiddit/sv: - modules/tiddit/sv/** - tests/modules/tiddit/sv/** diff --git a/tests/modules/tiddit/cov/main.nf b/tests/modules/tiddit/cov/main.nf new file mode 100644 index 00000000..aed3516c --- /dev/null +++ b/tests/modules/tiddit/cov/main.nf @@ -0,0 +1,23 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { TIDDIT_COV } from '../../../../modules/tiddit/cov/main.nf' addParams( options: [:] ) + +workflow test_tiddit_cov { + + input = [ [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] + + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + + TIDDIT_COV ( input, fasta ) +} + +workflow test_tiddit_cov_no_ref { + + input = [ [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] + + TIDDIT_COV ( input, [] ) +} diff --git a/tests/modules/tiddit/cov/test.yml b/tests/modules/tiddit/cov/test.yml new file mode 100644 index 00000000..c2aa6439 --- /dev/null +++ b/tests/modules/tiddit/cov/test.yml @@ -0,0 +1,17 @@ +- name: tiddit cov test_tiddit_cov + command: nextflow run tests/modules/tiddit/cov -entry test_tiddit_cov -c tests/config/nextflow.config + tags: + - tiddit + - tiddit/cov + files: + - path: output/tiddit/test.tab + md5sum: f7974948f809f94879d8a60b726194f5 + +- name: tiddit cov test_tiddit_cov_no_ref + command: nextflow run tests/modules/tiddit/cov -entry test_tiddit_cov_no_ref -c tests/config/nextflow.config + tags: + - tiddit + - tiddit/cov + files: + - path: output/tiddit/test.tab + md5sum: f7974948f809f94879d8a60b726194f5