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102 lines
3.6 KiB
Groovy
102 lines
3.6 KiB
Groovy
//
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// This file holds several functions specific to the main.nf workflow in the nf-core/taxprofiler pipeline
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//
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import nextflow.Nextflow
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class WorkflowMain {
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//
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// Citation string for pipeline
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//
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public static String citation(workflow) {
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return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
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// TODO nf-core: Add Zenodo DOI for pipeline after first release
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//"* The pipeline\n" +
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//" https://doi.org/10.5281/zenodo.XXXXXXX\n\n" +
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'* The nf-core framework\n' +
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' https://doi.org/10.1038/s41587-020-0439-x\n\n' +
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'* Software dependencies\n' +
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" https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
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}
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//
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// Generate help string
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//
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public static String help(workflow, params) {
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def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker"
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def help_string = ''
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help_string += NfcoreTemplate.logo(workflow, params.monochrome_logs)
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help_string += NfcoreSchema.paramsHelp(workflow, params, command)
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help_string += '\n' + citation(workflow) + '\n'
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help_string += NfcoreTemplate.dashedLine(params.monochrome_logs)
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return help_string
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}
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//
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// Generate parameter summary log string
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//
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public static String paramsSummaryLog(workflow, params) {
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def summary_log = ''
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summary_log += NfcoreTemplate.logo(workflow, params.monochrome_logs)
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summary_log += NfcoreSchema.paramsSummaryLog(workflow, params)
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summary_log += '\n' + citation(workflow) + '\n'
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summary_log += NfcoreTemplate.dashedLine(params.monochrome_logs)
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return summary_log
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}
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//
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// Validate parameters and print summary to screen
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//
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public static void initialise(workflow, params, log) {
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// Print help to screen if required
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if (params.help) {
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log.info help(workflow, params)
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System.exit(0)
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}
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// Print workflow version and exit on --version
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if (params.version) {
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String workflow_version = NfcoreTemplate.version(workflow)
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log.info "${workflow.manifest.name} ${workflow_version}"
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System.exit(0)
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}
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// Print parameter summary log to screen
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log.info paramsSummaryLog(workflow, params)
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// Validate workflow parameters via the JSON schema
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if (params.validate_params) {
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NfcoreSchema.validateParameters(workflow, params, log)
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}
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// Check that a -profile or Nextflow config has been provided to run the pipeline
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NfcoreTemplate.checkConfigProvided(workflow, log)
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// Check that conda channels are set-up correctly
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if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
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Utils.checkCondaChannels(log)
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}
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// Check AWS batch settings
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NfcoreTemplate.awsBatch(workflow, params)
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// Check input has been provided
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if (!params.input) {
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Nextflow.error("Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'")
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}
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}
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//
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// Get attribute from genome config file e.g. fasta
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//
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public static Object getGenomeAttribute(params, attribute) {
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if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
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if (params.genomes[ params.genome ].containsKey(attribute)) {
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return params.genomes[ params.genome ][ attribute ]
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}
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}
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return null
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}
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}
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