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1455498152
* Make targets.bed optional when running in wgs mode * added test for cram * Update test_data_config with new reference.cnn * Update main.nf to allow tumor-only running Still need a unit-test for this. Almost ready, but needs this file as input https://github.com/nf-core/test-datasets/blob/modules/data/generic/cnn/reference.cnn * re-writing previous changes, but now it wont crash the entire CI-setup * fixing overlooked merge conflict * last overlooked merge-conflict * move all files to batch subfolder * adding an optional input for a reference file (needed when running germline and tumoronly) * minor typo * update meta.yml * aligning code, renaming cnvkit to cnvkit_batch, renaming tumorbam to tumor, normalbam to normal * Update pytest_modules.yml Co-authored-by: EC2 Default User <ec2-user@ip-172-31-21-198.us-west-2.compute.internal> Co-authored-by: Lasse Folkersen <lassefolkersen@gmail.com> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
78 lines
2.6 KiB
Text
Executable file
78 lines
2.6 KiB
Text
Executable file
//
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// Utility functions used in nf-core DSL2 module files
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//
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//
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// Extract name of software tool from process name using $task.process
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//
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def getSoftwareName(task_process) {
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return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
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}
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//
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// Extract name of module from process name using $task.process
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//
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def getProcessName(task_process) {
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return task_process.tokenize(':')[-1]
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}
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//
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// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
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//
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def initOptions(Map args) {
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def Map options = [:]
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options.args = args.args ?: ''
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options.args2 = args.args2 ?: ''
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options.args3 = args.args3 ?: ''
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options.publish_by_meta = args.publish_by_meta ?: []
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options.publish_dir = args.publish_dir ?: ''
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options.publish_files = args.publish_files
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options.suffix = args.suffix ?: ''
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return options
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}
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//
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// Tidy up and join elements of a list to return a path string
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//
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def getPathFromList(path_list) {
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def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
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paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
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return paths.join('/')
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}
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//
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// Function to save/publish module results
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//
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def saveFiles(Map args) {
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def ioptions = initOptions(args.options)
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def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
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// Do not publish versions.yml unless running from pytest workflow
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if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
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return null
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}
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if (ioptions.publish_by_meta) {
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def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
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for (key in key_list) {
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if (args.meta && key instanceof String) {
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def path = key
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if (args.meta.containsKey(key)) {
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path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
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}
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path = path instanceof String ? path : ''
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path_list.add(path)
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}
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}
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}
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if (ioptions.publish_files instanceof Map) {
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for (ext in ioptions.publish_files) {
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if (args.filename.endsWith(ext.key)) {
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def ext_list = path_list.collect()
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ext_list.add(ext.value)
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return "${getPathFromList(ext_list)}/$args.filename"
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}
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}
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} else if (ioptions.publish_files == null) {
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return "${getPathFromList(path_list)}/$args.filename"
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}
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}
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