diff --git a/.github/workflows/fastp.yml b/.github/workflows/fastp.yml new file mode 100644 index 00000000..90ad15ef --- /dev/null +++ b/.github/workflows/fastp.yml @@ -0,0 +1,40 @@ +name: fastp +on: + push: + paths: + - software/fastp/** + - .github/workflows/fastp.yml + - tests + pull_request: + paths: + - software/fastp/** + - .github/workflows/fastp.yml + - tests + +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 fastp --symlink --wt 2 diff --git a/software/fastp/functions.nf b/software/fastp/functions.nf new file mode 100644 index 00000000..d25eea86 --- /dev/null +++ b/software/fastp/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)}/$args.filename" + } + } +} diff --git a/software/fastp/main.nf b/software/fastp/main.nf new file mode 100644 index 00000000..a9d048cf --- /dev/null +++ b/software/fastp/main.nf @@ -0,0 +1,72 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName } from './functions' + +params.options = [:] +def options = initOptions(params.options) + +process FASTP { + tag "$meta.id" + label 'process_medium' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + + conda (params.enable_conda ? 'bioconda::fastp=0.20.1' : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container 'https://depot.galaxyproject.org/singularity/fastp:0.20.1--h8b12597_0' + } else { + container 'quay.io/biocontainers/fastp:0.20.1--h8b12597_0' + } + + input: + tuple val(meta), path(reads) + + output: + tuple val(meta), path('*.trim.fastq.gz'), emit: reads + tuple val(meta), path('*.json') , emit: json + tuple val(meta), path('*.html') , emit: html + tuple val(meta), path('*.log') , emit: log + path '*.version.txt' , emit: version + tuple val(meta), path('*.fail.fastq.gz'), optional:true, emit: reads_fail + + script: + // Added soft-links to original fastqs for consistent naming in MultiQC + def software = getSoftwareName(task.process) + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + if (meta.single_end) { + def fail_fastq = params.save_trimmed_fail ? "--failed_out ${prefix}.fail.fastq.gz" : '' + """ + [ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz + fastp \\ + --in1 ${prefix}.fastq.gz \\ + --out1 ${prefix}.trim.fastq.gz \\ + --thread $task.cpus \\ + --json ${prefix}.fastp.json \\ + --html ${prefix}.fastp.html \\ + $fail_fastq \\ + $options.args \\ + 2> ${prefix}.fastp.log + echo \$(fastp --version 2>&1) | sed -e "s/fastp //g" > ${software}.version.txt + """ + } else { + def fail_fastq = params.save_trimmed_fail ? "--unpaired1 ${prefix}_1.fail.fastq.gz --unpaired2 ${prefix}_2.fail.fastq.gz" : '' + """ + [ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz + [ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz + fastp \\ + --in1 ${prefix}_1.fastq.gz \\ + --in2 ${prefix}_2.fastq.gz \\ + --out1 ${prefix}_1.trim.fastq.gz \\ + --out2 ${prefix}_2.trim.fastq.gz \\ + --json ${prefix}.fastp.json \\ + --html ${prefix}.fastp.html \\ + $fail_fastq \\ + --thread $task.cpus \\ + --detect_adapter_for_pe \\ + $options.args \\ + 2> ${prefix}.fastp.log + + echo \$(fastp --version 2>&1) | sed -e "s/fastp //g" > ${software}.version.txt + """ + } +} diff --git a/software/fastp/meta.yml b/software/fastp/meta.yml new file mode 100644 index 00000000..2846d834 --- /dev/null +++ b/software/fastp/meta.yml @@ -0,0 +1,79 @@ +name: fastp +description: Perform adapter/quality trimming on sequencing reads +keywords: + - trimming + - quality control + - fastq +tools: + - fastq: + description: | + A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. + documentation: https://github.com/OpenGene/fastp + doi: https://doi.org/10.1093/bioinformatics/bty560 +params: + - outdir: + type: string + description: | + The pipeline's output directory. By default, the module will + output files into `$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: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: The trimmed/modified fastq reads + pattern: "*trim.fastq.gz" + - json: + type: file + description: Results in JSON format + pattern: "*.json" + - html: + type: file + description: Results in HTML format + pattern: "*.thml" + - log: + type: file + description: fastq log file + pattern: "*.log" + - version: + type: file + description: File containing software version + pattern: "*.{version.txt}" + - reads_fail: + type: file + description: Reads the failed the preprocessing + pattern: "*fail.fastq.gz" +authors: + - "@drpatelh" + - "@kevinmenden" diff --git a/tests/software/fastp/main.nf b/tests/software/fastp/main.nf new file mode 100644 index 00000000..000fcdd8 --- /dev/null +++ b/tests/software/fastp/main.nf @@ -0,0 +1,30 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { FASTP } from '../../../software/fastp/main.nf' addParams( options: [:] ) + +/* + * Test with single-end data + */ +workflow test_fastp_se { + def input = [] + input = [ [ id:'test', single_end:true ], // meta map + [ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ] + + FASTP( input ) +} + +/* + * Test with paired-end data + */ + +workflow test_fastp_pe { + def input = [] + input = [ [ id:'test', single_end:false ], // meta map + [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true), + file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ] + + FASTP( input ) +} + diff --git a/tests/software/fastp/test.yml b/tests/software/fastp/test.yml new file mode 100644 index 00000000..56cbcaa7 --- /dev/null +++ b/tests/software/fastp/test.yml @@ -0,0 +1,27 @@ +- name: fastp_se + command: nextflow run ./tests/software/fastp -profile docker -entry test_fastp_se -c ./tests/config/nextflow.config + tags: + - fastp + - fastp_se + files: + - path: ./output/fastp/test.fastp.json + md5sum: b81d53bfa5c1553bed89f6475edcf437 + - path: ./output/fastp/test.trim.fastq.gz + md5sum: 2f5516df477b123e3f78adb67effa3bc + - path: ./output/fastp/test.fastp.log + - path: ./output/fastp/test.fastp.html + +- name: fastp_pe + command: nextflow run ./tests/software/fastp -profile docker -entry test_fastp_pe -c ./tests/config/nextflow.config + tags: + - fastp + - fastp_pe + files: + - path: ./output/fastp/test.fastp.html + - path: ./output/fastp/test.fastp.json + md5sum: 40db7fcbed478b0a96a1c5c1bb5f737b + - path: ./output/fastp/test.fastp.log + - path: ./output/fastp/test_1.trim.fastq.gz + md5sum: c8844c05194b50ae368e6825e997aa7f + - path: ./output/fastp/test_2.trim.fastq.gz + md5sum: 9238b07bb1609e939be7c8889b72c209