From bd8ba42a8da632e655fe73775e84920772050e24 Mon Sep 17 00:00:00 2001 From: kevinmenden Date: Fri, 19 Feb 2021 12:41:29 +0100 Subject: [PATCH 1/2] added gatk4 SamToFastq --- .github/filters.yml | 4 ++ software/gatk4/samtofastq/functions.nf | 59 ++++++++++++++++++++++++ software/gatk4/samtofastq/main.nf | 40 ++++++++++++++++ software/gatk4/samtofastq/meta.yml | 56 ++++++++++++++++++++++ tests/software/gatk4/samtofastq/main.nf | 23 +++++++++ tests/software/gatk4/samtofastq/test.yml | 19 ++++++++ 6 files changed, 201 insertions(+) create mode 100644 software/gatk4/samtofastq/functions.nf create mode 100644 software/gatk4/samtofastq/main.nf create mode 100644 software/gatk4/samtofastq/meta.yml create mode 100644 tests/software/gatk4/samtofastq/main.nf create mode 100644 tests/software/gatk4/samtofastq/test.yml diff --git a/.github/filters.yml b/.github/filters.yml index 537d982f..888a0838 100644 --- a/.github/filters.yml +++ b/.github/filters.yml @@ -128,6 +128,10 @@ gatk_createsequencedictionary: - software/gatk/createsequencedictionary/** - tests/software/gatk/createsequencedictionary/** +gatk4_samtofastq: + - software/gatk4/samtofastq/** + - tests/software/gatk4/samtofastq/** + gffread: - software/gffread/** - tests/software/gffread/** diff --git a/software/gatk4/samtofastq/functions.nf b/software/gatk4/samtofastq/functions.nf new file mode 100644 index 00000000..d25eea86 --- /dev/null +++ b/software/gatk4/samtofastq/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)}/$args.filename" + } + } +} diff --git a/software/gatk4/samtofastq/main.nf b/software/gatk4/samtofastq/main.nf new file mode 100644 index 00000000..04164f3f --- /dev/null +++ b/software/gatk4/samtofastq/main.nf @@ -0,0 +1,40 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName } from './functions' + +params.options = [:] +def options = initOptions(params.options) + +process GATK4_SAMTOFASTQ { + tag "$meta.id" + label 'process_medium' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + + conda (params.enable_conda ? 'bioconda::gatk4:4.1.9.0' : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container 'https://depot.galaxyproject.org/singularity/gatk4:4.1.9.0--py39_0' + } else { + container 'quay.io/biocontainers/gatk4:4.1.9.0--py39_0' + } + + input: + tuple val(meta), path(bam) + + output: + tuple val(meta), path('*.fastq.gz') , emit: fastq + path '*.version.txt' , emit: version + + script: + def software = getSoftwareName(task.process) + def prefix = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}" + def output = meta.single_end ? "FASTQ=${prefix}.fastq.gz" : "FASTQ=${prefix}_1.fastq.gz SECOND_END_FASTQ=${prefix}_2.fastq.gz" + """ + gatk SamToFastq \\ + I=$bam \\ + $output \\ + $options.args + + gatk --version | grep Picard | sed "s/Picard Version: //g" > ${software}.version.txt + """ +} diff --git a/software/gatk4/samtofastq/meta.yml b/software/gatk4/samtofastq/meta.yml new file mode 100644 index 00000000..8d8d2336 --- /dev/null +++ b/software/gatk4/samtofastq/meta.yml @@ -0,0 +1,56 @@ +name: gatk4_samtofastq +description: Converts BAM/SAM file to FastQ format +keywords: + - bed + - interval list +tools: + - gatk4: + description: | + Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools + with a primary focus on variant discovery and genotyping. Its powerful processing engine + and high-performance computing features make it capable of taking on projects of any size. + homepage: https://gatk.broadinstitute.org/hc/en-us + documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s + doi: 10.1158/1538-7445.AM2017-3590 +params: + - outdir: + type: string + description: | + The pipeline's output directory. By default, the module will + output files into `$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'] + - bam: + type: file + description: Input SAM/BAM file + pattern: "*.{bam,sam}" +output: + - fastq: + type: file + description: converted fastq file + pattern: "*.fastq" + - version: + type: file + description: File containing software version + pattern: "*.version.txt" +authors: + - "@kevinmenden" diff --git a/tests/software/gatk4/samtofastq/main.nf b/tests/software/gatk4/samtofastq/main.nf new file mode 100644 index 00000000..7c64783e --- /dev/null +++ b/tests/software/gatk4/samtofastq/main.nf @@ -0,0 +1,23 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { GATK4_SAMTOFASTQ } from '../../../../software/gatk4/samtofastq/main.nf' addParams( options: [:] ) + +workflow test_gatk4_samtofastq_single_end { + + def input = [] + input = [ [ id:'test', single_end: true ], // meta map + [ file("${launchDir}/tests/data/bam/test.single_end.sorted.bam", checkIfExists: true)] ] + + GATK4_SAMTOFASTQ ( input ) +} + +workflow test_gatk4_samtofastq_paired_end { + + def input = [] + input = [ [ id:'test', single_end: false ], // meta map + [ file("${launchDir}/tests/data/bam/test.single_end.sorted.bam", checkIfExists: true)] ] + + GATK4_SAMTOFASTQ ( input ) +} diff --git a/tests/software/gatk4/samtofastq/test.yml b/tests/software/gatk4/samtofastq/test.yml new file mode 100644 index 00000000..242fd934 --- /dev/null +++ b/tests/software/gatk4/samtofastq/test.yml @@ -0,0 +1,19 @@ +- name: gatk4 samtofastq single-end + command: nextflow run ./tests/software/gatk4/samtofastq -entry test_gatk4_samtofastq_single_end -c tests/config/nextflow.config + tags: + - gatk4 + - gatk4_samtofastq_single_end + files: + - path: output/gatk4/test.fastq.gz + md5sum: 61c6d3556ac6e0d09d800415b9a48508 + +- name: gatk4 samtofastq paired-end + command: nextflow run ./tests/software/gatk4/samtofastq -entry test_gatk4_samtofastq_paired_end -c tests/config/nextflow.config + tags: + - gatk4 + - gatk4_samtofastq_paired_end + files: + - path: output/gatk4/test_1.fastq.gz + md5sum: 61c6d3556ac6e0d09d800415b9a48508 + - path: output/gatk4/test_2.fastq.gz + md5sum: d0e74ab8dccca91c0ccd7125e588d5cd From 908e55ee5c7b302ed377d84fca2f6df16dca0194 Mon Sep 17 00:00:00 2001 From: kevinmenden Date: Fri, 19 Feb 2021 12:46:59 +0100 Subject: [PATCH 2/2] fixed tag --- tests/software/gatk4/samtofastq/test.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/tests/software/gatk4/samtofastq/test.yml b/tests/software/gatk4/samtofastq/test.yml index 242fd934..026b2c35 100644 --- a/tests/software/gatk4/samtofastq/test.yml +++ b/tests/software/gatk4/samtofastq/test.yml @@ -2,6 +2,7 @@ command: nextflow run ./tests/software/gatk4/samtofastq -entry test_gatk4_samtofastq_single_end -c tests/config/nextflow.config tags: - gatk4 + - gatk4_samtofastq - gatk4_samtofastq_single_end files: - path: output/gatk4/test.fastq.gz @@ -11,6 +12,7 @@ command: nextflow run ./tests/software/gatk4/samtofastq -entry test_gatk4_samtofastq_paired_end -c tests/config/nextflow.config tags: - gatk4 + - gatk4_samtofastq - gatk4_samtofastq_paired_end files: - path: output/gatk4/test_1.fastq.gz