mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
16e8d21477
* add nanoplot * add Nanopore 100 read subset bam and fastq * add nanoplot module and sequencing_summary.txt * Update pytest_software.yml * Update main.nf * test directory path * testing one output file * Update main.nf * fix typo * remove path to test outputs (it worked locally) * use test_data.config in test * add meta.yml * allowing either summary.txt or fastq.gz inputs * fix linting and test.yml * test whether github check can catch the output * add summary.txt test output paths * check Nanoplot-report.html output
59 lines
2 KiB
Text
59 lines
2 KiB
Text
/*
|
|
* -----------------------------------------------------
|
|
* Utility functions used in nf-core DSL2 module files
|
|
* -----------------------------------------------------
|
|
*/
|
|
|
|
/*
|
|
* Extract name of software tool from process name using $task.process
|
|
*/
|
|
def getSoftwareName(task_process) {
|
|
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
|
}
|
|
|
|
/*
|
|
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
|
*/
|
|
def initOptions(Map args) {
|
|
def Map options = [:]
|
|
options.args = args.args ?: ''
|
|
options.args2 = args.args2 ?: ''
|
|
options.publish_by_id = args.publish_by_id ?: false
|
|
options.publish_dir = args.publish_dir ?: ''
|
|
options.publish_files = args.publish_files
|
|
options.suffix = args.suffix ?: ''
|
|
return options
|
|
}
|
|
|
|
/*
|
|
* Tidy up and join elements of a list to return a path string
|
|
*/
|
|
def getPathFromList(path_list) {
|
|
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
|
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
|
return paths.join('/')
|
|
}
|
|
|
|
/*
|
|
* Function to save/publish module results
|
|
*/
|
|
def saveFiles(Map args) {
|
|
if (!args.filename.endsWith('.version.txt')) {
|
|
def ioptions = initOptions(args.options)
|
|
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
|
if (ioptions.publish_by_id) {
|
|
path_list.add(args.publish_id)
|
|
}
|
|
if (ioptions.publish_files instanceof Map) {
|
|
for (ext in ioptions.publish_files) {
|
|
if (args.filename.endsWith(ext.key)) {
|
|
def ext_list = path_list.collect()
|
|
ext_list.add(ext.value)
|
|
return "${getPathFromList(ext_list)}/$args.filename"
|
|
}
|
|
}
|
|
} else if (ioptions.publish_files == null) {
|
|
return "${getPathFromList(path_list)}/$args.filename"
|
|
}
|
|
}
|
|
}
|