From 23f9284aaecf77c8f3ddd3f447109a06bd588917 Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Thu, 21 Jan 2021 16:34:49 -0600 Subject: [PATCH] Added dsh-bio split-bed as dsh_splitbed --- .github/workflows/dsh_splitbed.yml | 40 ++++++++++++++++++++ software/dsh/splitbed/functions.nf | 59 ++++++++++++++++++++++++++++++ software/dsh/splitbed/main.nf | 42 +++++++++++++++++++++ software/dsh/splitbed/meta.yml | 59 ++++++++++++++++++++++++++++++ tests/software/dsh/main.nf | 10 +++++ tests/software/dsh/test.yml | 11 ++++++ 6 files changed, 221 insertions(+) create mode 100644 .github/workflows/dsh_splitbed.yml create mode 100644 software/dsh/splitbed/functions.nf create mode 100644 software/dsh/splitbed/main.nf create mode 100644 software/dsh/splitbed/meta.yml diff --git a/.github/workflows/dsh_splitbed.yml b/.github/workflows/dsh_splitbed.yml new file mode 100644 index 00000000..f2ebbd88 --- /dev/null +++ b/.github/workflows/dsh_splitbed.yml @@ -0,0 +1,40 @@ +name: dsh_splitbed +on: + push: + paths: + - software/dsh/splitbed/** + - .github/workflows/dsh_splitbed.yml + - tests/software/dsh/** + pull_request: + paths: + - software/dsh/splitbed/** + - .github/workflows/dsh_splitbed.yml + - tests/software/dsh/** + +jobs: + ci_test: + runs-on: ubuntu-latest + strategy: + matrix: + nxf_version: [20.11.0-edge] + env: + NXF_ANSI_LOG: false + steps: + - uses: actions/checkout@v2 + + - name: Install Nextflow + env: + NXF_VER: ${{ matrix.nxf_version }} + run: | + wget -qO- get.nextflow.io | bash + sudo mv nextflow /usr/local/bin/ + + - name: Set up Python + uses: actions/setup-python@v2 + with: + python-version: "3.x" + - name: Install dependencies + run: python -m pip install --upgrade pip pytest-workflow + + # Test the module + - run: pytest --tag dsh_splitbed --symlink --wt 2 diff --git a/software/dsh/splitbed/functions.nf b/software/dsh/splitbed/functions.nf new file mode 100644 index 00000000..d25eea86 --- /dev/null +++ b/software/dsh/splitbed/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)}/$args.filename" + } + } +} diff --git a/software/dsh/splitbed/main.nf b/software/dsh/splitbed/main.nf new file mode 100644 index 00000000..713b4215 --- /dev/null +++ b/software/dsh/splitbed/main.nf @@ -0,0 +1,42 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName } from './functions' + +params.options = [:] +def options = initOptions(params.options) + +process DSH_SPLITBED { + tag "${meta.id}" + label 'process_medium' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + + conda (params.enable_conda ? "bioconda::dsh-bio=1.4" : null) + + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/dsh-bio:1.4--0" + } else { + container "quay.io/biocontainers/dsh-bio:1.4--0" + } + + input: + tuple val(meta), path(features) + + output: + tuple val(meta), path("*.bed.gz"), emit: features + path "*.version.txt" , emit: version + + script: + def software = getSoftwareName(task.process) + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + + """ + dsh-split-bed \\ + $options.args \\ + -p $prefix \\ + -s '.bed.gz' \\ + -i $features + + echo \$(dsh-bio --version 2>&1) | grep -o 'dsh-bio-tools .*' | cut -f2 -d ' ' > ${software}.version.txt + """ +} diff --git a/software/dsh/splitbed/meta.yml b/software/dsh/splitbed/meta.yml new file mode 100644 index 00000000..91444648 --- /dev/null +++ b/software/dsh/splitbed/meta.yml @@ -0,0 +1,59 @@ +name: dsh_splitbed +description: Split features in gzipped BED format +keywords: + - bed +tools: + - dsh: + description: | + Reads, features, variants, assemblies, alignments, genomic range trees, pangenome + graphs, and a bunch of random command line tools for bioinformatics. LGPL version 3 + or later. + homepage: https://github.com/heuermh/dishevelled-bio + documentation: https://github.com/heuermh/dishevelled-bio +params: + - outdir: + type: string + description: | + The pipeline's output directory. By default, the module will + output files into `$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 ] + - features: + type: file + description: Features in gzipped BED format to split + pattern: "*.{bed.gz}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - features: + type: file + description: Features in split gzipped BED formatted files + pattern: "*.{bed.gz}" + - version: + type: file + description: File containing software version + pattern: "*.{version.txt}" +authors: + - "@heuermh" diff --git a/tests/software/dsh/main.nf b/tests/software/dsh/main.nf index e22ae054..e007e3e1 100644 --- a/tests/software/dsh/main.nf +++ b/tests/software/dsh/main.nf @@ -3,6 +3,7 @@ nextflow.enable.dsl = 2 include { DSH_FILTERBED } from '../../../software/dsh/filterbed/main.nf' addParams( options: [suffix: '.filtered', args: '--range chr1:0-1000'] ) +include { DSH_SPLITBED } from '../../../software/dsh/splitbed/main.nf' addParams( options: [suffix: '.', args: '--records 2'] ) workflow test_dsh_filterbed { @@ -12,3 +13,12 @@ workflow test_dsh_filterbed { DSH_FILTERBED ( input ) } + +workflow test_dsh_splitbed { + + def input = [] + input = [ [ id:'A' ], // meta map + [ file("${launchDir}/tests/data/bed/A.bed.gz", checkIfExists: true) ] ] + + DSH_SPLITBED ( input ) +} diff --git a/tests/software/dsh/test.yml b/tests/software/dsh/test.yml index e6dde73b..3e4261b7 100644 --- a/tests/software/dsh/test.yml +++ b/tests/software/dsh/test.yml @@ -6,3 +6,14 @@ files: - path: output/dsh/A.filtered.bed.gz md5sum: 91cee4392d6034793f99f6c53891d866 + +- name: Run dsh splitbed + command: nextflow run ./tests/software/dsh -profile docker -entry test_dsh_splitbed -c tests/config/nextflow.config + tags: + - dsh + - dsh_splitbed + files: + - path: output/dsh/A.0.bed.gz + md5sum: 619e51c435d0e7138ca41b660ed07e3a + - path: output/dsh/A.1.bed.gz + md5sum: 223bba025a0bb859de9a1bf385550a7e