Functions
This page documents helper functions defined in the pipeline.
Contents
- paramsSummaryMultiqc
- validateInputParameters
- validateInputSamplesheet
- checkSamplesAfterGrouping
- genomeExistsError
- toolCitationText
- toolBibliographyText
- methodsDescriptionText
- isCloudUrl
- isCompatibleStarIndex
- convertVersionToList
paramsSummaryMultiqc
Defined in main.nf:327
def paramsSummaryMultiqc(summary_params)
Parameters
| Name | Description | Default |
|---|---|---|
summary_params |
- | - |
validateInputParameters
Defined in subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf:251
def validateInputParameters()
Validate pipeline input parameters. Checks that all required parameters are provided and valid. Currently validates that the specified genome exists in the config.
validateInputSamplesheet
Defined in subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf:264
def validateInputSamplesheet(input)
Validate and parse input samplesheet entries. Ensures that multiple runs of the same sample have consistent sequencing type (all single-end or all paired-end).
Parameters
| Name | Description | Default |
|---|---|---|
input |
- | - |
checkSamplesAfterGrouping
Defined in subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf:288
def checkSamplesAfterGrouping(input)
Validate samples after grouping by sample ID. Performs consistency checks on grouped sample data:
- Ensures only one BAM/CRAM file per sample
- Prevents mixing of FASTQ and BAM/CRAM inputs
- Validates consistent single-end/paired-end status
- Properly interleaves paired-end FASTQ files
Parameters
| Name | Description | Default |
|---|---|---|
input |
- | - |
genomeExistsError
Defined in subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf:343
def genomeExistsError()
Check if the specified genome exists in the configuration. Throws an error with a helpful message listing available genomes if the specified genome key is not found in the config.
toolCitationText
Defined in subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf:353
def toolCitationText()
toolBibliographyText
Defined in subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf:367
def toolBibliographyText()
methodsDescriptionText
Defined in subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf:379
def methodsDescriptionText(mqc_methods_yaml)
Parameters
| Name | Description | Default |
|---|---|---|
mqc_methods_yaml |
- | - |
isCloudUrl
Defined in subworkflows/local/annotation_cache_initialisation/main.nf:70
def isCloudUrl(cache_url)
Parameters
| Name | Description | Default |
|---|---|---|
cache_url |
- | - |
isCompatibleStarIndex
Defined in subworkflows/local/prepare_genome/main.nf:263
def isCompatibleStarIndex(index_version, minimal_index_version)
Parameters
| Name | Description | Default |
|---|---|---|
index_version |
- | - |
minimal_index_version |
- | - |
convertVersionToList
Defined in subworkflows/local/prepare_genome/main.nf:299
def convertVersionToList(version)
Parameters
| Name | Description | Default |
|---|---|---|
version |
- | - |
This pipeline was built with Nextflow. Documentation generated by nf-docs v0.1.0 on 2026-01-23 17:23:12 UTC.