Functions¶

This page documents helper functions defined in the pipeline.

Contents¶

parseTcrEpitopeSamplesheet
buildNmfVaeSamplesChannel
buildBatchEffectAssessmentsSamplesChannel
buildIngestExportSamplesChannel
buildTcrMilSamplesChannel
buildMakeTcrVectorDatabaseSamplesChannel
buildIngestTabulateSamplesChannel
buildIntegrationPipelineSamplesChannel
buildGexMilSamplesChannel

parseTcrEpitopeSamplesheet¶

Defined in workflows/tcr_epitope_pipeline.nf:28

def parseTcrEpitopeSamplesheet(samplesheetPath)

Parameters¶

Name	Description	Default
`samplesheetPath`	-	-

buildNmfVaeSamplesChannel¶

Defined in workflows/nmf_vae.nf:20

def buildNmfVaeSamplesChannel(samplesheetPath)

Build the metadata channel consumed by the NMF-VAE workflow. The samplesheet must define one row per sample with the columns sample_id, species, lambda_graph, and one of output_file_id (LabKey mode), url (public download mode), or path (local-file mode).

Parameters¶

Name	Description	Default
`samplesheetPath`	-	-

buildBatchEffectAssessmentsSamplesChannel¶

Defined in workflows/batch_effect_assessments_pipeline.nf:20

def buildBatchEffectAssessmentsSamplesChannel(samplesheetPath)

Parameters¶

Name	Description	Default
`samplesheetPath`	-	-

buildIngestExportSamplesChannel¶

Defined in workflows/ingest_export.nf:18

def buildIngestExportSamplesChannel(samplesheetPath)

Build the samplesheet-derived metadata channel for the ingest/export workflow. The samplesheet must define one row per sample with the columns sample_id, species, and one of output_file_id (LabKey mode), url (public download mode), or path (local-file mode).

Parameters¶

Name	Description	Default
`samplesheetPath`	-	-

buildTcrMilSamplesChannel¶

Defined in workflows/tcr_mil_pipeline.nf:22

def buildTcrMilSamplesChannel(samplesheetPath)

Parameters¶

Name	Description	Default
`samplesheetPath`	-	-

buildMakeTcrVectorDatabaseSamplesChannel¶

Defined in workflows/make_tcr_vector_database_pipeline.nf:23

def buildMakeTcrVectorDatabaseSamplesChannel(samplesheetPath)

Parameters¶

Name	Description	Default
`samplesheetPath`	-	-

buildIngestTabulateSamplesChannel¶

Defined in workflows/ingest_tabulate.nf:19

def buildIngestTabulateSamplesChannel(samplesheetPath)

Build the samplesheet-derived metadata channel for the metadata-only path. The samplesheet must define one row per sample with the columns sample_id, species, and one of output_file_id (LabKey mode), url (public download mode), path (local-file mode), or metadata_path (metadata CSV mode).

Parameters¶

Name	Description	Default
`samplesheetPath`	-	-

buildIntegrationPipelineSamplesChannel¶

Defined in workflows/integration_pipeline.nf:20

def buildIntegrationPipelineSamplesChannel(samplesheetPath)

Build the metadata channel consumed by the integration multi-species workflow. The samplesheet must define one row per sample with the columns sample_id, species, and one of output_file_id (LabKey mode), url (public download mode), or path (local-file mode).

Parameters¶

Name	Description	Default
`samplesheetPath`	-	-

buildGexMilSamplesChannel¶

Defined in workflows/gex_mil_pipeline.nf:23

def buildGexMilSamplesChannel(samplesheetPath)

Parameters¶

Name	Description	Default
`samplesheetPath`	-	-

This pipeline was built with Nextflow. Documentation generated by nf-docs v0.4.0 on 2026-06-03 23:27:50 UTC.