From a740a6ff4890be1abb4d4cb3f67c0cd332bd11d7 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 26 Oct 2021 22:54:10 +0200 Subject: [PATCH] New module: `checkm/lineagewf` (#899) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * feat: add megahit module, currently decompressed output * Update main.nf * Update tests/modules/megahit/test.yml Co-authored-by: Maxime Borry * Apply suggestions from code review Co-authored-by: Harshil Patel * feat: compress all outputs, remove md5sums due to gz stochasicity * fix: wrong conda channel for pigz * fix: broken singleend tests and update meta.yml * Missed one * Apply suggestions from code review Co-authored-by: Harshil Patel * fix: pigz formatting * Apply suggestions from code review Co-authored-by: Harshil Patel * Apply suggestions from code review * Added but test failing due to null on output channel * fix prefix variable * Complete checkm_lineagewf * Remove TODOs * Add description of fasta_ext parameter * Improve meta map for this context * Update meta.yml * Update modules/checkm/lineagewf/meta.yml Co-authored-by: James A. Fellows Yates * Update main.nf Co-authored-by: Harshil Patel Co-authored-by: Maxime Borry Co-authored-by: Daniel Lundin --- modules/checkm/lineagewf/functions.nf | 78 +++++++++++++++++++++++++ modules/checkm/lineagewf/main.nf | 49 ++++++++++++++++ modules/checkm/lineagewf/meta.yml | 58 ++++++++++++++++++ tests/config/pytest_modules.yml | 6 +- tests/modules/checkm/lineagewf/main.nf | 24 ++++++++ tests/modules/checkm/lineagewf/test.yml | 35 +++++++++++ 6 files changed, 249 insertions(+), 1 deletion(-) create mode 100644 modules/checkm/lineagewf/functions.nf create mode 100644 modules/checkm/lineagewf/main.nf create mode 100644 modules/checkm/lineagewf/meta.yml create mode 100644 tests/modules/checkm/lineagewf/main.nf create mode 100644 tests/modules/checkm/lineagewf/test.yml diff --git a/modules/checkm/lineagewf/functions.nf b/modules/checkm/lineagewf/functions.nf new file mode 100644 index 00000000..85628ee0 --- /dev/null +++ b/modules/checkm/lineagewf/functions.nf @@ -0,0 +1,78 @@ +// +// 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() +} + +// +// Extract name of module from process name using $task.process +// +def getProcessName(task_process) { + return task_process.tokenize(':')[-1] +} + +// +// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules +// +def initOptions(Map args) { + def Map options = [:] + options.args = args.args ?: '' + options.args2 = args.args2 ?: '' + options.args3 = args.args3 ?: '' + options.publish_by_meta = args.publish_by_meta ?: [] + options.publish_dir = args.publish_dir ?: '' + options.publish_files = args.publish_files + options.suffix = args.suffix ?: '' + return options +} + +// +// Tidy up and join elements of a list to return a path string +// +def getPathFromList(path_list) { + def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries + paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes + return paths.join('/') +} + +// +// Function to save/publish module results +// +def saveFiles(Map args) { + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${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)}/$args.filename" + } +} diff --git a/modules/checkm/lineagewf/main.nf b/modules/checkm/lineagewf/main.nf new file mode 100644 index 00000000..e655e5f5 --- /dev/null +++ b/modules/checkm/lineagewf/main.nf @@ -0,0 +1,49 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' + +params.options = [:] +options = initOptions(params.options) + +process CHECKM_LINEAGEWF { + tag "$meta.id" + label 'process_medium' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } + + conda (params.enable_conda ? "bioconda::checkm-genome=1.1.3" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/checkm-genome:1.1.3--py_1" + } else { + container "quay.io/biocontainers/checkm-genome:1.1.3--py_1" + } + + input: + tuple val(meta), path(fasta) + val fasta_ext + + output: + tuple val(meta), path("${prefix}") , emit: checkm_output + tuple val(meta), path("${prefix}.tsv"), emit: checkm_tsv + path "versions.yml" , emit: versions + + script: + prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + """ + checkm \\ + lineage_wf \\ + -t $task.cpus \\ + -f ${prefix}.tsv \\ + --tab_table \\ + --pplacer_threads $task.cpus \\ + -x $fasta_ext \\ + $options.args \\ + . \\ + $prefix + + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$( checkm 2>&1 | grep '...:::' | sed 's/.*CheckM v//;s/ .*//' ) + END_VERSIONS + """ +} diff --git a/modules/checkm/lineagewf/meta.yml b/modules/checkm/lineagewf/meta.yml new file mode 100644 index 00000000..29c6096e --- /dev/null +++ b/modules/checkm/lineagewf/meta.yml @@ -0,0 +1,58 @@ +name: checkm_lineagewf +description: CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. +keywords: + - checkm + - mag + - metagenome + - quality + - isolates + - microbes + - single cells + - completeness + - contamination + - bins + - genome bins +tools: + - checkm: + description: Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes. + homepage: https://ecogenomics.github.io/CheckM/ + documentation: https://github.com/Ecogenomics/CheckM/wiki + tool_dev_url: https://github.com/Ecogenomics/CheckM + doi: "10.1101/gr.186072.114" + licence: ['GPL v3'] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: One or a list of multiple FASTA files of each bin, with extension defined with the fasta_ext value + pattern: "*.{$fasta_ext}" + - fasta_ext: + type: value + description: The file-type extension suffix of the input FASTA files (e.g., fasta, fna, fa, fas) + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample', bin:'1' ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - checkm_output: + type: directory + description: CheckM output directory + pattern: "*/" + - checkm_tsv: + type: file + description: CheckM summary completeness statistics table + pattern: "*.tsv" + +authors: + - "@jfy133" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 4e35fa24..343a0fc2 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -254,6 +254,10 @@ cat/fastq: - modules/cat/fastq/** - tests/modules/cat/fastq/** +checkm/lineagewf: + - modules/checkm/lineagewf/** + - tests/modules/checkm/lineagewf/** + chromap/chromap: - modules/chromap/chromap/** - tests/modules/chromap/chromap/** @@ -1106,7 +1110,7 @@ ucsc/bigwigaverageoverbed: ucsc/liftover: - modules/ucsc/liftover/** - tests/modules/ucsc/liftover/** - + ucsc/wigtobigwig: - modules/ucsc/wigtobigwig/** - tests/modules/ucsc/wigtobigwig/** diff --git a/tests/modules/checkm/lineagewf/main.nf b/tests/modules/checkm/lineagewf/main.nf new file mode 100644 index 00000000..94309896 --- /dev/null +++ b/tests/modules/checkm/lineagewf/main.nf @@ -0,0 +1,24 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { CHECKM_LINEAGEWF } from '../../../../modules/checkm/lineagewf/main.nf' addParams( options: [:] ) + +workflow test_checkm_lineagewf { + + input = [ [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true) ] + fasta_ext = 'fasta' + + CHECKM_LINEAGEWF ( input, fasta_ext ) +} + +workflow test_checkm_lineagewf_multi { + + input = [ [ id:'test', single_end:false ], // meta map + [ file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true), + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] ] + fasta_ext = 'fasta' + + CHECKM_LINEAGEWF ( input, fasta_ext ) +} diff --git a/tests/modules/checkm/lineagewf/test.yml b/tests/modules/checkm/lineagewf/test.yml new file mode 100644 index 00000000..768601b0 --- /dev/null +++ b/tests/modules/checkm/lineagewf/test.yml @@ -0,0 +1,35 @@ +- name: checkm lineagewf + command: nextflow run ./tests/modules/checkm/lineagewf -entry test_checkm_lineagewf -c tests/config/nextflow.config + tags: + - checkm + - checkm/lineagewf + files: + - path: output/checkm/test.tsv + md5sum: d5559764f563c4b55223e4e4a3dc1ec9 + - path: output/checkm/test/checkm.log + contains: + - "INFO: Parsing HMM hits to marker genes:" + - path: output/checkm/test/lineage.ms + contains: + - "# [Lineage Marker File]" + - "contigs" + - "UID1" + +- name: checkm lineagewf_multi + command: nextflow run ./tests/modules/checkm/lineagewf -entry test_checkm_lineagewf_multi -c tests/config/nextflow.config + tags: + - checkm + - checkm/lineagewf + files: + - path: output/checkm/test.tsv + md5sum: 7e0fa177dcf151b84b7751813fbde3d1 + - path: output/checkm/test/checkm.log + contains: + - "INFO: Parsing HMM hits to marker genes:" + - path: output/checkm/test/lineage.ms + contains: + - "# [Lineage Marker File]" + - "contigs" + - "UID1" + - "genome" +