diff --git a/modules/maxquant/lfq/functions.nf b/modules/maxquant/lfq/functions.nf new file mode 100644 index 00000000..da9da093 --- /dev/null +++ b/modules/maxquant/lfq/functions.nf @@ -0,0 +1,68 @@ +// +// 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)}/$args.filename" + } + } +} diff --git a/modules/maxquant/lfq/main.nf b/modules/maxquant/lfq/main.nf new file mode 100644 index 00000000..41f6631d --- /dev/null +++ b/modules/maxquant/lfq/main.nf @@ -0,0 +1,63 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName } from './functions' + +// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters. +// All other parameters MUST be provided as a string i.e. "options.args" +// where "params.options" is a Groovy Map that MUST be provided via the addParams section of the including workflow. +// Any parameters that need to be evaluated in the context of a particular sample +// e.g. single-end/paired-end data MUST also be defined and evaluated appropriately. + +params.options = [:] +options = initOptions(params.options) + +process MAXQUANT_LFQ { + tag "$meta.id" + label 'process_long' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } + + conda (params.enable_conda ? "bioconda::maxquant=2.0.1.0" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/https://depot.galaxyproject.org/singularity/maxquant:2.0.1.0--py39hdfd78af_2" + } else { + container "quay.io/biocontainers/quay.io/biocontainers/maxquant:2.0.1.0--py39hdfd78af_2" + } + + input: + // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group" + // MUST be provided as an input via a Groovy Map called "meta". + // This information may not be required in some instances e.g. indexing reference genome files: + // https://github.com/nf-core/modules/blob/master/software/bwa/index/main.nf + // TODO nf-core: Where applicable please provide/convert compressed files as input/output + // e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc. + tuple val(meta), path(raw), path(paramfile) + + output: + // TODO nf-core: Named file extensions MUST be emitted for ALL output channels + tuple val(meta), path("combined/txt/*.txt"), emit: maxquant_txt + // TODO nf-core: List additional required output channels/values here + path "*.version.txt" , emit: version + + script: + def software = getSoftwareName(task.process) + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10 + // If the software is unable to output a version number on the command-line then it can be manually specified + // e.g. https://github.com/nf-core/modules/blob/master/software/homer/annotatepeaks/main.nf + // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "$options.args" variable + // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter + // using the Nextflow "task" variable e.g. "--threads $task.cpus" + // TODO nf-core: Please replace the example samtools command below with your module's command + // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;) + """ + maxquant --version > maxquant.version.txt + # Write number of threads into parameter file + sed "s_\.*_\12\<\/numThreads\>_" ${paramfile} + # Correct folder names + sed -i "s|PLACEHOLDER|\$PWD/|g" "${paramfile}" + mkdir temp + + maxquant ${paramfile} + """ +} diff --git a/modules/maxquant/lfq/meta.yml b/modules/maxquant/lfq/meta.yml new file mode 100644 index 00000000..4498d8ef --- /dev/null +++ b/modules/maxquant/lfq/meta.yml @@ -0,0 +1,47 @@ +name: maxquant_lfq +## TODO nf-core: Add a description of the module and list keywords +description: write your description here +keywords: + - sort +tools: + - maxquant: + ## TODO nf-core: Add a description and other details for the software below + description: MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. License restricted. + homepage: None + documentation: None + tool_dev_url: None + doi: "" + licence: ['http://www.coxdocs.org/lib/exe/fetch.php?media=license_agreement.pdf'] + +## TODO nf-core: Add a description of all of the variables used as input +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + ## TODO nf-core: Delete / customise this example input + - parfile: + type: file + description: MaxQuant parameter file (XML) + pattern: "*.{xml}" + +## TODO nf-core: Add a description of all of the variables used as output +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - version: + type: file + description: File containing software version + pattern: "*.{version.txt}" + ## TODO nf-core: Delete / customise this example output + - maxquant_txt: + type: file + description: tables with peptides and protein information + pattern: "*.{txt}" + +authors: + - "@veitveit"