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Add PSMRescoring、PSMFDRControl、Phosphoscoring、ProteinInference、Featur…
…emapper 、ProteinQuant subworkflow
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,47 @@ | ||
| // Import generic module functions | ||
| include { initOptions; saveFiles; getSoftwareName } from './functions' | ||
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| params.options = [:] | ||
| options = initOptions(params.options) | ||
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| process CONSENSUSID { | ||
| label 'process_medium' | ||
| // TODO could be easily parallelized | ||
| label 'process_single_thread' | ||
| publishDir "${params.outdir}", | ||
| mode: params.publish_dir_mode, | ||
| saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) } | ||
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| conda (params.enable_conda ? "openms::openms=2.7.0pre" : null) | ||
| if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { | ||
| container "https://depot.galaxyproject.org/singularity/openms:2.6.0--h4afb90d_0" | ||
| } else { | ||
| container "quay.io/biocontainers/openms:2.6.0--h4afb90d_0" | ||
| } | ||
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| input: | ||
| tuple val(meta), path(id_file) | ||
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| output: | ||
| tuple val(meta), path("${meta.id}_consensus.idXML"), emit: consensusids | ||
| path "*.version.txt", emit: version | ||
| path "*.log", emit: log | ||
| script: | ||
| def software = getSoftwareName(task.process) | ||
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| """ | ||
| ConsensusID \\ | ||
| -in ${id_file} \\ | ||
| -out ${meta.id}_consensus.idXML \\ | ||
| -per_spectrum \\ | ||
| -threads $task.cpus \\ | ||
| -algorithm $params.consensusid_algorithm \\ | ||
| -filter:min_support $params.min_consensus_support \\ | ||
| -filter:considered_hits $params.consensusid_considered_top_hits \\ | ||
| -debug 100 \\ | ||
| $options.args \\ | ||
| > ${meta.id}_consensusID.log | ||
| echo \$(ConsensusID 2>&1) > ${software}.version.txt | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,38 @@ | ||
| name: consensusid | ||
| description: Computes a consensus from results of multiple peptide identification engines. | ||
| keywords: | ||
| - FDR | ||
| - decoy | ||
| - OpenMS | ||
| tools: | ||
| - ConsensusID : | ||
| description: | | ||
| Tool to Computes a consensus from results of multiple peptide identification engines. | ||
| homepage: https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_ConsensusID.html | ||
| documentation: https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_ConsensusID.html | ||
| input: | ||
| - meta: | ||
| type: map | ||
| description: Groovy Map containing sample information | ||
| - id_file: | ||
| type: file | ||
| description: | | ||
| Identifications from searching a target-decoy database. | ||
| output: | ||
| - meta: | ||
| type: map | ||
| description: Groovy Map containing sample information | ||
| - id_files_idx_ForIDPEP_FDR: | ||
| type: file | ||
| description: | | ||
| Identifications with annotated FDR. | ||
| - log: | ||
| type: file | ||
| description: log file | ||
| pattern: "*.log" | ||
| - version: | ||
| type: file | ||
| description: File containing software version | ||
| pattern: "*.{version.txt}" | ||
| authors: | ||
| - "@daichengxin" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,68 @@ | ||
| // | ||
| // Utility functions used in nf-core DSL2 module files | ||
| // | ||
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| // | ||
| // Extract name of software tool from process name using $task.process | ||
| // | ||
| def getSoftwareName(task_process) { | ||
| return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() | ||
| } | ||
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| // | ||
| // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules | ||
| // | ||
| def initOptions(Map args) { | ||
| def Map options = [:] | ||
| options.args = args.args ?: '' | ||
| options.args2 = args.args2 ?: '' | ||
| options.args3 = args.args3 ?: '' | ||
| options.publish_by_meta = args.publish_by_meta ?: [] | ||
| options.publish_dir = args.publish_dir ?: '' | ||
| options.publish_files = args.publish_files | ||
| options.suffix = args.suffix ?: '' | ||
| return options | ||
| } | ||
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| // | ||
| // Tidy up and join elements of a list to return a path string | ||
| // | ||
| def getPathFromList(path_list) { | ||
| def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries | ||
| paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes | ||
| return paths.join('/') | ||
| } | ||
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| // | ||
| // Function to save/publish module results | ||
| // | ||
| def saveFiles(Map args) { | ||
| if (!args.filename.endsWith('.version.txt')) { | ||
| def ioptions = initOptions(args.options) | ||
| def path_list = [ ioptions.publish_dir ?: args.publish_dir ] | ||
| if (ioptions.publish_by_meta) { | ||
| def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta | ||
| for (key in key_list) { | ||
| if (args.meta && key instanceof String) { | ||
| def path = key | ||
| if (args.meta.containsKey(key)) { | ||
| path = args.meta[key] instanceof Boolean ? "${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" | ||
| } | ||
| } | ||
| } |
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