From d5f2f5e32dd75ec3138b7afe54ee97aae6df4169 Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Thu, 4 Feb 2021 13:42:08 -0600 Subject: [PATCH] Add minimap2 align module --- .github/filters.yml | 4 ++ software/minimap2/align/functions.nf | 59 +++++++++++++++++++++++ software/minimap2/align/main.nf | 57 ++++++++++++++++++++++ software/minimap2/align/meta.yml | 67 ++++++++++++++++++++++++++ tests/software/minimap2/align/main.nf | 37 ++++++++++++++ tests/software/minimap2/align/test.yml | 28 +++++++++++ 6 files changed, 252 insertions(+) create mode 100644 software/minimap2/align/functions.nf create mode 100644 software/minimap2/align/main.nf create mode 100644 software/minimap2/align/meta.yml create mode 100644 tests/software/minimap2/align/main.nf create mode 100644 tests/software/minimap2/align/test.yml diff --git a/.github/filters.yml b/.github/filters.yml index a9fb3498..be5cdf05 100644 --- a/.github/filters.yml +++ b/.github/filters.yml @@ -48,6 +48,10 @@ gffread: - software/gffread/** - tests/software/gffread/** +minimap2_align: + - software/minimap2/align/** + - tests/software/minimap2/align/** + multiqc: - software/fastqc/** - software/multiqc/** diff --git a/software/minimap2/align/functions.nf b/software/minimap2/align/functions.nf new file mode 100644 index 00000000..d25eea86 --- /dev/null +++ b/software/minimap2/align/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)}/$args.filename" + } + } +} diff --git a/software/minimap2/align/main.nf b/software/minimap2/align/main.nf new file mode 100644 index 00000000..1005f98a --- /dev/null +++ b/software/minimap2/align/main.nf @@ -0,0 +1,57 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName } from './functions' + +params.options = [:] +def options = initOptions(params.options) + +process MINIMAP2_ALIGN { + tag "$meta.id" + label 'process_medium' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + + conda (params.enable_conda ? "bioconda::minimap2=2.17=hed695b0_3" : null) + + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/minimap2:2.17--hed695b0_3" + } else { + container "quay.io/biocontainers/minimap2:2.17--hed695b0_3" + } + + input: + tuple val(meta), path(reads) + path reference + + output: + tuple val(meta), path("*.paf"), emit: paf + path "*.version.txt" , emit: version + + script: + def software = getSoftwareName(task.process) + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + if (meta.single_end) { + """ + minimap2 \\ + $options.args \\ + -t $task.cpus \\ + $reference \\ + $reads \\ + > ${prefix}.paf + + echo \$(minimap2 --version 2>&1) > ${software}.version.txt + """ + } else { + """ + minimap2 \\ + $options.args \\ + -t $task.cpus \\ + $reference \\ + ${reads[0]} \\ + ${reads[1]} \\ + > ${prefix}.paf + + echo \$(minimap2 --version 2>&1) > ${software}.version.txt + """ + } +} \ No newline at end of file diff --git a/software/minimap2/align/meta.yml b/software/minimap2/align/meta.yml new file mode 100644 index 00000000..a1daf6a3 --- /dev/null +++ b/software/minimap2/align/meta.yml @@ -0,0 +1,67 @@ +name: minimap2_align +description: A versatile pairwise aligner for genomic and spliced nucleotide sequences +keywords: + - align + - fasta + - fastq + - genome + - paf + - reference +tools: + - minimap2: + description: | + A versatile pairwise aligner for genomic and spliced nucleotide sequences. + homepage: https://github.com/lh3/minimap2 + documentation: https://github.com/lh3/minimap2#uguide +params: + - outdir: + type: string + description: | + The pipeline's output directory. By default, the module will + output files into `$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. + - reference: + type: file + description: | + Reference database in FASTA format. +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - paf: + type: file + description: Alignment in PAF format + pattern: "*.paf" + - version: + type: file + description: File containing software version + pattern: "*.{version.txt}" +authors: + - "@heuermh" diff --git a/tests/software/minimap2/align/main.nf b/tests/software/minimap2/align/main.nf new file mode 100644 index 00000000..1f35f5a6 --- /dev/null +++ b/tests/software/minimap2/align/main.nf @@ -0,0 +1,37 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { MINIMAP2_ALIGN } from '../../../../software/minimap2/align/main.nf' addParams( options: [:] ) + +workflow test_minimap2_align_single_end { + + def fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) + + def input = [] + input = [ [ id:'test', single_end:true ], // meta map + [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ] + MINIMAP2_ALIGN ( input, fasta ) +} + +workflow test_minimap2_align_paired_end { + + def fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) + + def input = [] + input = [ [ id:'test', single_end:false ], // meta map + [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true), + file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ] + MINIMAP2_ALIGN ( input, fasta ) +} + +workflow test_minimap2_align_pairwise { + + def fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) + + def input = [] + input = [ [ id:'test', single_end:false ], // meta map + [ fasta ] ] + + MINIMAP2_ALIGN ( input, fasta ) +} diff --git a/tests/software/minimap2/align/test.yml b/tests/software/minimap2/align/test.yml new file mode 100644 index 00000000..f7ca2375 --- /dev/null +++ b/tests/software/minimap2/align/test.yml @@ -0,0 +1,28 @@ +- name: minimap2 align single-end + command: nextflow run ./tests/software/minimap2/align -entry test_minimap2_align_single_end -c tests/config/nextflow.config + tags: + - minimap2 + - minimap2_align + - minimap2_align_single_end + files: + - path: output/minimap2/test.paf + md5: f92567a67adb0563bd6ff9ed97877be9 + +- name: minimap2 align paired-end + command: nextflow run ./tests/software/minimap2/align -entry test_minimap2_align_paired_end -c tests/config/nextflow.config + tags: + - minimap2 + - minimap2_align + - minimap2_align_paired_end + files: + - path: output/minimap2/test.paf + md5: b57e4009b113dcd48755cb713f613942 + +- name: minimap2 align pairwise + command: nextflow run ./tests/software/minimap2/align -entry test_minimap2_align_pairwise -c tests/config/nextflow.config + tags: + - minimap2 + - minimap2_align + - minimap2_align_pairwise + files: + - path: output/minimap2/test.paf