From ca321ce69d3cf167e8057c0d6fc075b089a769c5 Mon Sep 17 00:00:00 2001 From: Charles Plessy Date: Tue, 8 Jun 2021 18:14:08 +0900 Subject: [PATCH] New module last/postmask to filter alignment files (#526) The `last-postmask` tool distributed with [LAST](https://gitlab.com/mcfrith/last) filters alignments in a MAF file to remove those with too many masked (lower-case) positions compared with their score. As other filter modules like `last/split`, its output file risks to overwrite its input file as their names are constructed from the sample ID when multiple filters are chained in the pipeline. I added a check that gives a clearer error message in this case. Please let me know what you think about; I can add this test to the existing LAST modules as well. This new module is part of the work discribed in Issue #464. During this development, we fix the version of LAST to 1219 to ensure consistency. We will upgrade it later. --- software/last/postmask/functions.nf | 70 +++++++++++++++++++++++++++ software/last/postmask/main.nf | 38 +++++++++++++++ software/last/postmask/meta.yml | 39 +++++++++++++++ tests/config/pytest_software.yml | 4 ++ tests/software/last/postmask/main.nf | 13 +++++ tests/software/last/postmask/test.yml | 8 +++ 6 files changed, 172 insertions(+) create mode 100644 software/last/postmask/functions.nf create mode 100644 software/last/postmask/main.nf create mode 100644 software/last/postmask/meta.yml create mode 100644 tests/software/last/postmask/main.nf create mode 100644 tests/software/last/postmask/test.yml diff --git a/software/last/postmask/functions.nf b/software/last/postmask/functions.nf new file mode 100644 index 00000000..9d0137e3 --- /dev/null +++ b/software/last/postmask/functions.nf @@ -0,0 +1,70 @@ +/* + * ----------------------------------------------------- + * Utility functions used in nf-core DSL2 module files + * ----------------------------------------------------- + */ + +/* + * Extract name of software tool from process name using $task.process + */ +def getSoftwareName(task_process) { + return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() +} + +/* + * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules + */ +def initOptions(Map args) { + def Map options = [:] + options.args = args.args ?: '' + options.args2 = args.args2 ?: '' + options.args3 = args.args3 ?: '' + options.publish_by_meta = args.publish_by_meta ?: [] + options.publish_dir = args.publish_dir ?: '' + options.publish_files = args.publish_files + options.suffix = args.suffix ?: '' + return options +} + +/* + * Tidy up and join elements of a list to return a path string + */ +def getPathFromList(path_list) { + def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries + paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes + return paths.join('/') +} + +/* + * Function to save/publish module results + */ +def saveFiles(Map args) { + if (!args.filename.endsWith('.version.txt')) { + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${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)}/$args.filename" + } + } +} diff --git a/software/last/postmask/main.nf b/software/last/postmask/main.nf new file mode 100644 index 00000000..a31d0087 --- /dev/null +++ b/software/last/postmask/main.nf @@ -0,0 +1,38 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName } from './functions' + +params.options = [:] +options = initOptions(params.options) + +process LAST_POSTMASK { + tag "$meta.id" + label 'process_low' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } + + conda (params.enable_conda ? "bioconda::last=1219" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/last:1219--h2e03b76_0" + } else { + container "quay.io/biocontainers/last:1219--h2e03b76_0" + } + + input: + tuple val(meta), path(maf) + + output: + tuple val(meta), path("*.maf.gz"), emit: maf + path "*.version.txt" , emit: version + + script: + def software = getSoftwareName(task.process) + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + if( "$maf" == "${prefix}.maf.gz" ) error "Input and output names are the same, use the suffix option to disambiguate" + """ + zcat $maf | last-postmask $options.args | gzip --no-name > ${prefix}.maf.gz + + # last-postmask does not have a --version option + echo \$(lastal --version 2>&1) | sed 's/lastal //' > ${software}.version.txt + """ +} diff --git a/software/last/postmask/meta.yml b/software/last/postmask/meta.yml new file mode 100644 index 00000000..3b3cfcc1 --- /dev/null +++ b/software/last/postmask/meta.yml @@ -0,0 +1,39 @@ +name: last_postmask +description: Post-alignment masking +keywords: + - LAST + - mask + - alignment + - MAF +tools: + - last: + description: LAST finds & aligns related regions of sequences. + homepage: https://gitlab.com/mcfrith/last + documentation: https://gitlab.com/mcfrith/last/-/blob/main/doc/last-postmask.rst + tool_dev_url: https://gitlab.com/mcfrith/last + doi: "10.1371/journal.pone.0028819" + licence: ['GPL-3.0-or-later'] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - maf: + type: file + description: Multiple Aligment Format (MAF) file, compressed with gzip + pattern: "*.{maf.gz}" + +output: + - maf: + type: file + description: Multiple Aligment Format (MAF) file, compressed with gzip + pattern: "*.{maf.gz}" + - version: + type: file + description: File containing software version + pattern: "*.{version.txt}" + +authors: + - "@charles-plessy" diff --git a/tests/config/pytest_software.yml b/tests/config/pytest_software.yml index 069b3825..d602e79a 100644 --- a/tests/config/pytest_software.yml +++ b/tests/config/pytest_software.yml @@ -394,6 +394,10 @@ last/mafswap: - software/last/mafswap/** - tests/software/last/mafswap/** +last/postmask: + - software/last/postmask/** + - tests/software/last/postmask/** + last/split: - software/last/split/** - tests/software/last/split/** diff --git a/tests/software/last/postmask/main.nf b/tests/software/last/postmask/main.nf new file mode 100644 index 00000000..aafd3bfc --- /dev/null +++ b/tests/software/last/postmask/main.nf @@ -0,0 +1,13 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { LAST_POSTMASK } from '../../../../software/last/postmask/main.nf' addParams( options: [suffix:'.postmask'] ) + +workflow test_last_postmask { + + input = [ [ id:'contigs.genome' ], // meta map + file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) ] + + LAST_POSTMASK ( input ) +} diff --git a/tests/software/last/postmask/test.yml b/tests/software/last/postmask/test.yml new file mode 100644 index 00000000..1ca73c9a --- /dev/null +++ b/tests/software/last/postmask/test.yml @@ -0,0 +1,8 @@ +- name: last postmask test_last_postmask + command: nextflow run tests/software/last/postmask -entry test_last_postmask -c tests/config/nextflow.config + tags: + - last + - last/postmask + files: + - path: output/last/contigs.genome.postmask.maf.gz + md5sum: 3a0f42e76da9549748983ac4d7ff7473