Parameters
Complete reference for all --param flags accepted by main.nf. Defaults are set in configs/base.config. The machine-readable version of this reference is nextflow_schema.json.
| Parameter |
Default |
Description |
--workflow |
full |
Named workflow to execute. One of full, ingest_export, ingest_tabulate. |
--input |
data/samplesheet.csv |
Path to the samplesheet CSV. See Data Formats → Samplesheet. |
--outdir |
outputs/ |
Directory where published results are written. |
LabKey / Prime-seq options
These are required for all three workflows.
| Parameter |
Default |
Description |
--labkey_base_url |
(required) |
Base URL of the LabKey server (e.g. https://labkey.example.org). |
--labkey_folder |
(required) |
LabKey folder path (e.g. /My/Project/Folder). |
Species options
| Parameter |
Default |
Description |
--species_order |
human,macaque,mouse |
Comma-separated list of species. Controls the ordering during harmonization and scMODAL integration. Each value must match the species column in the samplesheet. |
--export_assay |
RNA |
Seurat assay name to export as count matrix in EXPORT_COUNTS. |
Tabulation options
These parameters affect only --workflow ingest_tabulate.
| Parameter |
Default |
Description |
--tabulate_id_cols |
cDNA_ID,SubjectId,Vaccine,Timepoint,Tissue |
Comma-separated subject-level identity columns to carry into subjectIdTable.csv. cDNA_ID is always included as the primary sample key. |
--tabulate_celltype_cols |
(empty) |
Extra cell-type annotation columns to tabulate beyond the standard RIRA set. Leave empty to use only the standard RIRA columns auto-detected in the metadata. |
--tabulate_parent_col |
(empty) |
Parent lineage column used to gate child cell-type columns. Defaults to RIRA_Immune.cellclass when empty. |
--tabulate_celltype_parent_map |
(empty) |
Comma-separated celltype_col:parentValue pairs to extend or override the built-in hierarchy. Example: RIRA_TNK_v2.cellclass:TNK,RIRA_Myeloid_v3.cellclass:Myeloid. |
scMODAL integration options
These parameters affect only --workflow full.
| Parameter |
Default |
Description |
--scmodal_container |
ghcr.io/gwmcelfresh/scmodal-cuda:latest |
Container image for GENE_HARMONIZE and SCMODAL_INTEGRATE. Must include scmodal, torch, scanpy, and anndata. |
--scmodal_latent |
20 |
Number of latent dimensions in the scMODAL VAE embedding. |
--scmodal_training_steps |
10000 |
Number of VAE training steps. Increase for larger datasets. |
--scmodal_batch_size |
500 |
Mini-batch size during scMODAL training. |
--scmodal_neighbors |
30 |
Number of nearest neighbours for the KNN graph built on the latent embedding. |
--leiden_resolution |
0.5 |
Leiden clustering resolution. Higher values produce more clusters. |
CI / testing options
Not for production use
--scmodal_use_cpu is intended exclusively for GitHub Actions smoke tests.
Using it outside CI will produce stub outputs with no scientific validity and will print a warning.
| Parameter |
Default |
Description |
--scmodal_use_cpu |
false |
Bypasses the local-executor GPU guard for --workflow full and runs SCMODAL_INTEGRATE as a stub (requires -stub-run). Emits a warning if GITHUB_ACTIONS env is not set. |
Generic options
| Parameter |
Default |
Description |
--help |
false |
Print help text and exit. |