Functions
This page documents helper functions defined in the pipeline.
Contents
- getGenomeAttribute
- getFileSuffix
- addReadgroupToMeta
- flowcellLaneFromFastq
- readFirstLineOfFastq
- checkConfigProvided
- checkProfileProvided
- getWorkflowVersion
- processVersionsFromYAML
- workflowVersionToYAML
- softwareVersionsToYAML
- paramsSummaryMultiqc
- logColours
- getSingleReport
- completionEmail
- completionSummary
- imNotification
- dumpParametersToJSON
- checkCondaChannels
- isCloudUrl
- validateInputParameters
- genomeExistsError
- sparkAndBam
- toolCitationText
- toolBibliographyText
- methodsDescriptionText
- retrieveInput
getGenomeAttribute
Defined in main.nf:342
def getGenomeAttribute(attribute)
Parameters
| Name | Description | Default |
|---|---|---|
attribute |
- | - |
getFileSuffix
Defined in modules/nf-core/cat/cat/main.nf:75
def getFileSuffix(filename)
Parameters
| Name | Description | Default |
|---|---|---|
filename |
- | - |
addReadgroupToMeta
Defined in workflows/sarek/main.nf:631
def addReadgroupToMeta(meta, files)
Parameters
| Name | Description | Default |
|---|---|---|
meta |
- | - |
files |
- | - |
flowcellLaneFromFastq
Defined in workflows/sarek/main.nf:653
def flowcellLaneFromFastq(path)
Parameters
| Name | Description | Default |
|---|---|---|
path |
- | - |
readFirstLineOfFastq
Defined in workflows/sarek/main.nf:681
def readFirstLineOfFastq(path)
Parameters
| Name | Description | Default |
|---|---|---|
path |
- | - |
checkConfigProvided
Defined in subworkflows/nf-core/utils_nfcore_pipeline/main.nf:32
def checkConfigProvided()
checkProfileProvided
Defined in subworkflows/nf-core/utils_nfcore_pipeline/main.nf:46
def checkProfileProvided(nextflow_cli_args)
Parameters
| Name | Description | Default |
|---|---|---|
nextflow_cli_args |
- | - |
getWorkflowVersion
Defined in subworkflows/nf-core/utils_nfcore_pipeline/main.nf:62
def getWorkflowVersion()
processVersionsFromYAML
Defined in subworkflows/nf-core/utils_nfcore_pipeline/main.nf:80
def processVersionsFromYAML(yaml_file)
Parameters
| Name | Description | Default |
|---|---|---|
yaml_file |
- | - |
workflowVersionToYAML
Defined in subworkflows/nf-core/utils_nfcore_pipeline/main.nf:89
def workflowVersionToYAML()
softwareVersionsToYAML
Defined in subworkflows/nf-core/utils_nfcore_pipeline/main.nf:100
def softwareVersionsToYAML(ch_versions)
Parameters
| Name | Description | Default |
|---|---|---|
ch_versions |
- | - |
paramsSummaryMultiqc
Defined in subworkflows/nf-core/utils_nfcore_pipeline/main.nf:107
def paramsSummaryMultiqc(summary_params)
Parameters
| Name | Description | Default |
|---|---|---|
summary_params |
- | - |
logColours
Defined in subworkflows/nf-core/utils_nfcore_pipeline/main.nf:141
def logColours(monochrome_logs)
Parameters
| Name | Description | Default |
|---|---|---|
monochrome_logs |
- | - |
getSingleReport
Defined in subworkflows/nf-core/utils_nfcore_pipeline/main.nf:208
def getSingleReport(multiqc_reports)
Parameters
| Name | Description | Default |
|---|---|---|
multiqc_reports |
- | - |
completionEmail
Defined in subworkflows/nf-core/utils_nfcore_pipeline/main.nf:229
def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report)
Parameters
| Name | Description | Default |
|---|---|---|
summary_params |
- | - |
email |
- | - |
email_on_fail |
- | - |
plaintext_email |
- | - |
outdir |
- | - |
monochrome_logs |
- | - |
multiqc_report |
- | - |
completionSummary
Defined in subworkflows/nf-core/utils_nfcore_pipeline/main.nf:342
def completionSummary(monochrome_logs)
Parameters
| Name | Description | Default |
|---|---|---|
monochrome_logs |
- | - |
imNotification
Defined in subworkflows/nf-core/utils_nfcore_pipeline/main.nf:360
def imNotification(summary_params, hook_url)
Parameters
| Name | Description | Default |
|---|---|---|
summary_params |
- | - |
hook_url |
- | - |
dumpParametersToJSON
Defined in subworkflows/nf-core/utils_nextflow_pipeline/main.nf:73
def dumpParametersToJSON(outdir)
Parameters
| Name | Description | Default |
|---|---|---|
outdir |
- | - |
checkCondaChannels
Defined in subworkflows/nf-core/utils_nextflow_pipeline/main.nf:87
def checkCondaChannels()
isCloudUrl
Defined in subworkflows/local/annotation_cache_initialisation/main.nf:70
def isCloudUrl(cache_url)
Parameters
| Name | Description | Default |
|---|---|---|
cache_url |
- | - |
validateInputParameters
Defined in subworkflows/local/utils_nfcore_sarek_pipeline/main.nf:248
def validateInputParameters()
genomeExistsError
Defined in subworkflows/local/utils_nfcore_sarek_pipeline/main.nf:254
def genomeExistsError()
sparkAndBam
Defined in subworkflows/local/utils_nfcore_sarek_pipeline/main.nf:262
def sparkAndBam()
toolCitationText
Defined in subworkflows/local/utils_nfcore_sarek_pipeline/main.nf:271
def toolCitationText()
toolBibliographyText
Defined in subworkflows/local/utils_nfcore_sarek_pipeline/main.nf:285
def toolBibliographyText()
methodsDescriptionText
Defined in subworkflows/local/utils_nfcore_sarek_pipeline/main.nf:297
def methodsDescriptionText(mqc_methods_yaml)
Parameters
| Name | Description | Default |
|---|---|---|
mqc_methods_yaml |
- | - |
retrieveInput
Defined in subworkflows/local/utils_nfcore_sarek_pipeline/main.nf:338
def retrieveInput(need_input, step, outdir)
Parameters
| Name | Description | Default |
|---|---|---|
need_input |
- | - |
step |
- | - |
outdir |
- | - |
This pipeline was built with Nextflow. Documentation generated by nf-docs v0.1.0 on 2026-01-23 17:27:10 UTC.