Workflows¶
This page documents all workflows in the pipeline.
Contents¶
INGEST_TABULATE_PIPELINE¶
Defined in workflows/ingest_tabulate.nf:39
Metadata-only workflow entrypoint. Downloads cell-level metadata tables from LabKey and aggregates them into a subject-level summary table suitable for cohort QC and downstream analysis.
Inputs¶
| Name | Description |
|---|---|
samplesheet |
- |
Outputs¶
| Name | Description |
|---|---|
metadata |
- |
subject_table |
- |
FULL_PIPELINE¶
Defined in workflows/full_pipeline.nf:45
Full pipeline entrypoint. Downloads Seurat objects from LabKey, exports raw counts, harmonizes genes across species, and trains scMODAL to create a shared latent embedding. This workflow is GPU-backed and intended for SLURM execution.
Inputs¶
| Name | Description |
|---|---|
samplesheet |
- |
Outputs¶
| Name | Description |
|---|---|
rds |
- |
counts |
- |
harmonized |
- |
model |
- |
INGEST_EXPORT_PIPELINE¶
Defined in workflows/ingest_export.nf:39
Download Seurat objects and export them as 10x-like count directories. This workflow is intended for fast local or CI validation when users want count matrices without running cross-species harmonization or scMODAL.
Inputs¶
| Name | Description |
|---|---|
samplesheet |
- |
Outputs¶
| Name | Description |
|---|---|
rds |
- |
counts |
- |
This pipeline was built with Nextflow. Documentation generated by nf-docs v0.2.1 on 2026-04-16 21:10:06 UTC.