From 374d81e0b39d24ec2ef84b6f931c74ded5e3e682 Mon Sep 17 00:00:00 2001 From: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Date: Tue, 2 Nov 2021 11:01:13 +0000 Subject: [PATCH] readcounter module for hmmcopy (#1001) * readcounter module for hmmcopy * Changed version number * Fix indentation * Update main.nf * Update modules/hmmcopy/readcounter/main.nf Co-authored-by: Chris Cheshire Co-authored-by: Simon Pearce Co-authored-by: Chris Cheshire --- modules/hmmcopy/readcounter/functions.nf | 78 ++++++++++++++++++++++ modules/hmmcopy/readcounter/main.nf | 42 ++++++++++++ modules/hmmcopy/readcounter/meta.yml | 43 ++++++++++++ tests/config/pytest_modules.yml | 4 ++ tests/modules/hmmcopy/readcounter/main.nf | 14 ++++ tests/modules/hmmcopy/readcounter/test.yml | 8 +++ 6 files changed, 189 insertions(+) create mode 100644 modules/hmmcopy/readcounter/functions.nf create mode 100644 modules/hmmcopy/readcounter/main.nf create mode 100644 modules/hmmcopy/readcounter/meta.yml create mode 100644 tests/modules/hmmcopy/readcounter/main.nf create mode 100644 tests/modules/hmmcopy/readcounter/test.yml diff --git a/modules/hmmcopy/readcounter/functions.nf b/modules/hmmcopy/readcounter/functions.nf new file mode 100644 index 00000000..85628ee0 --- /dev/null +++ b/modules/hmmcopy/readcounter/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)}/$args.filename" + } +} diff --git a/modules/hmmcopy/readcounter/main.nf b/modules/hmmcopy/readcounter/main.nf new file mode 100644 index 00000000..9e3e72a7 --- /dev/null +++ b/modules/hmmcopy/readcounter/main.nf @@ -0,0 +1,42 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' + +params.options = [:] +options = initOptions(params.options) + +def VERSION = '0.1.1' + +process HMMCOPY_READCOUNTER { + tag "$meta.id" + label 'process_low' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } + + conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_5" + } else { + container "quay.io/biocontainers/hmmcopy:0.1.1--h2e03b76_5" + } + + input: + tuple val(meta), path(bam), path(bai) + + output: + tuple val(meta), path("*.wig"), emit: wig + path "versions.yml" , emit: versions + + script: + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + """ + readCounter \\ + $options.args \\ + ${bam} > ${prefix}.wig + + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$(echo $VERSION) + END_VERSIONS + """ +} diff --git a/modules/hmmcopy/readcounter/meta.yml b/modules/hmmcopy/readcounter/meta.yml new file mode 100644 index 00000000..9b09a55c --- /dev/null +++ b/modules/hmmcopy/readcounter/meta.yml @@ -0,0 +1,43 @@ +name: hmmcopy_readcounter +description: readCounter function from HMMcopy utilities, used to generate read in windows +keywords: + - hmmcopy + - readcounter + - cnv +tools: + - hmmcopy: + description: C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy + homepage: https://github.com/shahcompbio/hmmcopy_utils + documentation: https://github.com/shahcompbio/hmmcopy_utils + tool_dev_url: https://github.com/shahcompbio/hmmcopy_utils + doi: "" + 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/SAM file + pattern: "*.{bam,cram,sam}" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - wig: + type: file + description: A wig file with the number of reads lying within each window in each chromosome + pattern: "*.wig" + +authors: + - "@sppearce" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 4e4526b1..9320245f 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -581,6 +581,10 @@ hmmcopy/gccounter: - modules/hmmcopy/gccounter/** - tests/modules/hmmcopy/gccounter/** +hmmcopy/readcounter: + - modules/hmmcopy/readcounter/** + - tests/modules/hmmcopy/readcounter/** + hmmer/hmmalign: - modules/hmmer/hmmalign/** - tests/modules/hmmer/hmmalign/** diff --git a/tests/modules/hmmcopy/readcounter/main.nf b/tests/modules/hmmcopy/readcounter/main.nf new file mode 100644 index 00000000..9025f98e --- /dev/null +++ b/tests/modules/hmmcopy/readcounter/main.nf @@ -0,0 +1,14 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { HMMCOPY_READCOUNTER } from '../../../../modules/hmmcopy/readcounter/main.nf' addParams( options: [:] ) + +workflow test_hmmcopy_readcounter { + + input = [ [ id:'test'], // meta map + [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true)], + [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)] + ] + HMMCOPY_READCOUNTER ( input ) +} diff --git a/tests/modules/hmmcopy/readcounter/test.yml b/tests/modules/hmmcopy/readcounter/test.yml new file mode 100644 index 00000000..6c00ee08 --- /dev/null +++ b/tests/modules/hmmcopy/readcounter/test.yml @@ -0,0 +1,8 @@ +- name: hmmcopy readcounter test_hmmcopy_readcounter + command: nextflow run tests/modules/hmmcopy/readcounter -entry test_hmmcopy_readcounter -c tests/config/nextflow.config + tags: + - hmmcopy + - hmmcopy/readcounter + files: + - path: output/hmmcopy/test.wig + md5sum: 3655d8325baea81b3b690791262c6b57