mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 13:43:09 +00:00
906577873b
* New functions.nf * Convert code to create versions.yml * Update meta.yml * update output channel * Fix more meta.yml * Manually update remaining modules * remove superflous echo * Fix misformatted meta.yml files * Fix yaml, was list instead of dict * fix version for bcftools Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
78 lines
2.6 KiB
Text
78 lines
2.6 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()
|
|
}
|
|
|
|
//
|
|
// Extract name of module from process name using $task.process
|
|
//
|
|
def getProcessName(task_process) {
|
|
return task_process.tokenize(':')[-1]
|
|
}
|
|
|
|
//
|
|
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
|
//
|
|
def initOptions(Map args) {
|
|
def Map options = [:]
|
|
options.args = args.args ?: ''
|
|
options.args2 = args.args2 ?: ''
|
|
options.args3 = args.args3 ?: ''
|
|
options.publish_by_meta = args.publish_by_meta ?: []
|
|
options.publish_dir = args.publish_dir ?: ''
|
|
options.publish_files = args.publish_files
|
|
options.suffix = args.suffix ?: ''
|
|
return options
|
|
}
|
|
|
|
//
|
|
// Tidy up and join elements of a list to return a path string
|
|
//
|
|
def getPathFromList(path_list) {
|
|
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
|
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
|
return paths.join('/')
|
|
}
|
|
|
|
//
|
|
// Function to save/publish module results
|
|
//
|
|
def saveFiles(Map args) {
|
|
def ioptions = initOptions(args.options)
|
|
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
|
|
|
// Do not publish versions.yml unless running from pytest workflow
|
|
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
|
return null
|
|
}
|
|
if (ioptions.publish_by_meta) {
|
|
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
|
for (key in key_list) {
|
|
if (args.meta && key instanceof String) {
|
|
def path = key
|
|
if (args.meta.containsKey(key)) {
|
|
path = args.meta[key] instanceof Boolean ? "${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"
|
|
}
|
|
}
|