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kevinmenden 2020-12-18 11:11:19 +01:00
parent db0b631906
commit 32f6191ff3
2 changed files with 120 additions and 120 deletions
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120
software/bowtie/align/functions.nf
View file

@ -1,60 +1,60 @@
/* /*
* ----------------------------------------------------- * -----------------------------------------------------
* Utility functions used in nf-core DSL2 module files * Utility functions used in nf-core DSL2 module files
* ----------------------------------------------------- * -----------------------------------------------------
*/ */
/* /*
* Extract name of software tool from process name using $task.process * Extract name of software tool from process name using $task.process
*/ */
def getSoftwareName(task_process) { def getSoftwareName(task_process) {
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() 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 * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
*/ */
def initOptions(Map args) { def initOptions(Map args) {
def Map options = [:] def Map options = [:]
options.args = args.args ?: '' options.args = args.args ?: ''
options.args2 = args.args2 ?: '' options.args2 = args.args2 ?: ''
options.publish_by_id = args.publish_by_id ?: false options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: '' options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files options.publish_files = args.publish_files
options.suffix = args.suffix ?: '' options.suffix = args.suffix ?: ''
return options return options
} }
/* /*
* Tidy up and join elements of a list to return a path string * Tidy up and join elements of a list to return a path string
*/ */
def getPathFromList(path_list) { def getPathFromList(path_list) {
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", '') } // Trim whitespace and trailing slashes
return paths.join('/') return paths.join('/')
} }
/* /*
* Function to save/publish module results * Function to save/publish module results
*/ */
def saveFiles(Map args) { def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) { if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options) def ioptions = initOptions(args.options)
def path_list = [ ioptions.publish_dir ?: args.publish_dir ] def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
if (ioptions.publish_by_id) { if (ioptions.publish_by_id) {
path_list.add(args.publish_id) path_list.add(args.publish_id)
} }
if (ioptions.publish_files instanceof Map) { if (ioptions.publish_files instanceof Map) {
for (ext in ioptions.publish_files) { for (ext in ioptions.publish_files) {
if (args.filename.endsWith(ext.key)) { if (args.filename.endsWith(ext.key)) {
def ext_list = path_list.collect() def ext_list = path_list.collect()
ext_list.add(ext.value) ext_list.add(ext.value)
return "${getPathFromList(ext_list)}/$args.filename" return "${getPathFromList(ext_list)}/$args.filename"
} }
} }
} else if (ioptions.publish_files == null) { } else if (ioptions.publish_files == null) {
return "${getPathFromList(path_list)}/$args.filename" return "${getPathFromList(path_list)}/$args.filename"
} }
} }
} }

120
software/bowtie/index/functions.nf
View file

@ -1,60 +1,60 @@
/* /*
* ----------------------------------------------------- * -----------------------------------------------------
* Utility functions used in nf-core DSL2 module files * Utility functions used in nf-core DSL2 module files
* ----------------------------------------------------- * -----------------------------------------------------
*/ */
/* /*
* Extract name of software tool from process name using $task.process * Extract name of software tool from process name using $task.process
*/ */
def getSoftwareName(task_process) { def getSoftwareName(task_process) {
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() 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 * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
*/ */
def initOptions(Map args) { def initOptions(Map args) {
def Map options = [:] def Map options = [:]
options.args = args.args ?: '' options.args = args.args ?: ''
options.args2 = args.args2 ?: '' options.args2 = args.args2 ?: ''
options.publish_by_id = args.publish_by_id ?: false options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: '' options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files options.publish_files = args.publish_files
options.suffix = args.suffix ?: '' options.suffix = args.suffix ?: ''
return options return options
} }
/* /*
* Tidy up and join elements of a list to return a path string * Tidy up and join elements of a list to return a path string
*/ */
def getPathFromList(path_list) { def getPathFromList(path_list) {
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", '') } // Trim whitespace and trailing slashes
return paths.join('/') return paths.join('/')
} }
/* /*
* Function to save/publish module results * Function to save/publish module results
*/ */
def saveFiles(Map args) { def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) { if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options) def ioptions = initOptions(args.options)
def path_list = [ ioptions.publish_dir ?: args.publish_dir ] def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
if (ioptions.publish_by_id) { if (ioptions.publish_by_id) {
path_list.add(args.publish_id) path_list.add(args.publish_id)
} }
if (ioptions.publish_files instanceof Map) { if (ioptions.publish_files instanceof Map) {
for (ext in ioptions.publish_files) { for (ext in ioptions.publish_files) {
if (args.filename.endsWith(ext.key)) { if (args.filename.endsWith(ext.key)) {
def ext_list = path_list.collect() def ext_list = path_list.collect()
ext_list.add(ext.value) ext_list.add(ext.value)
return "${getPathFromList(ext_list)}/$args.filename" return "${getPathFromList(ext_list)}/$args.filename"
} }
} }
} else if (ioptions.publish_files == null) { } else if (ioptions.publish_files == null) {
return "${getPathFromList(path_list)}/$args.filename" return "${getPathFromList(path_list)}/$args.filename"
} }
} }
} }