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Update comments with new style (#497)

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* Update comment style on functions.nf files

* Update test main.nf comments

* Add meta for ggread
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Jose Espinosa-Carrasco 2021-05-12 15:56:46 +02:00 committed by GitHub
parent 598ca152ec
commit 95e02f913f
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32
software/abacas/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/adapterremoval/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/allelecounter/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/artic/guppyplex/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/artic/minion/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/bandage/image/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/bbmap/bbduk/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/bcftools/consensus/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/bcftools/filter/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/bcftools/isec/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/bcftools/merge/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/bcftools/mpileup/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/bcftools/stats/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/bedtools/bamtobed/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/bedtools/complement/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/bedtools/genomecov/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/bedtools/getfasta/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/bedtools/intersect/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/bedtools/maskfasta/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/bedtools/merge/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/bedtools/slop/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/bedtools/sort/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/bismark/align/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/bismark/deduplicate/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/bismark/genomepreparation/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/bismark/methylationextractor/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/bismark/report/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/bismark/summary/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/blast/blastn/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/blast/makeblastdb/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/bowtie/align/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/bowtie/build/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/bowtie2/align/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/bowtie2/build/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/bwa/index/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/bwa/mem/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/bwamem2/index/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/bwamem2/mem/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/bwameth/align/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/bwameth/index/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/cat/fastq/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/cnvkit/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/cutadapt/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/deeptools/computematrix/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/deeptools/plotfingerprint/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/deeptools/plotheatmap/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/deeptools/plotprofile/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/dshbio/filterbed/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/dshbio/filtergff3/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/dshbio/splitbed/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/dshbio/splitgff3/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/fastp/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/fastqc/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/fasttree/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/fgbio/callmolecularconsensusreads/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/fgbio/sortbam/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/flash/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/gatk4/applybqsr/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/gatk4/baserecalibrator/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/gatk4/bedtointervallist/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/gatk4/createsequencedictionary/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/gatk4/fastqtosam/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/gatk4/haplotypecaller/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

66
software/gatk4/intervallisttools/functions.nf
View file

@ -1,49 +1,57 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
options.args2 = args.args2 ?: ''
options.args3 = args.args3 ?: ''
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 ?: ''
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
*/
//
// 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
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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
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 ]
if (ioptions.publish_by_id) {
path_list.add(args.publish_id)
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) {

32
software/gatk4/markduplicates/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/gatk4/mergebamalignment/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/gatk4/mergevcfs/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/gatk4/revertsam/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/gatk4/samtofastq/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/gatk4/splitncigarreads/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/gatk4/variantfiltration/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/gffread/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

43
software/gffread/meta.yml Normal file
View file

@ -0,0 +1,43 @@
name: gffread
description: Validate, filter, convert and perform various other operations on GFF files
keywords:
- gff
- conversion
- validation
tools:
- gffread:
description: GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more.
homepage: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread
documentation: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread
tool_dev_url: https://github.com/gpertea/gffread
doi: 10.12688/f1000research.23297.1
licence: ['MIT']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- gff:
type: file
description: A GFF file in either the GFF3 or GFF2 format.
patter: "*.gff"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- gtf:
type: file
description: GTF file resulting from the conversion of the GFF input file
pattern: "*.gtf"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@emiller88"

32
software/graphmap2/align/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/graphmap2/index/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/gubbins/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/gunzip/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/hisat2/align/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/hisat2/build/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/hisat2/extractsplicesites/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/hmmer/hmmalign/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/homer/annotatepeaks/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/iqtree/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/ivar/consensus/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/ivar/trim/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/ivar/variants/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/kallisto/index/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

66
software/kallistobustools/count/functions.nf
View file

@ -1,49 +1,57 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
options.args2 = args.args2 ?: ''
options.args3 = args.args3 ?: ''
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 ?: ''
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
*/
//
// 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
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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
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 ]
if (ioptions.publish_by_id) {
path_list.add(args.publish_id)
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) {

32
software/kallistobustools/ref/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/kraken2/run/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/last/lastdb/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/lib/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/macs2/callpeak/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/mash/sketch/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/methyldackel/extract/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/methyldackel/mbias/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/minia/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/minimap2/align/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/minimap2/index/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

32
software/mosdepth/functions.nf
View file

@ -1,19 +1,17 @@
/*
* -----------------------------------------------------
* 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) {
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 Map options = [:]
options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
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 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
*/
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)

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