CLI reference¶
The installed command is the authoritative reference:
omnomnomics --help
omnomnomics rna --help
omnomnomics atac --help
omnomnomics chip --help
omnomnomics monitor --help
omnomnomics genomes --help
Common workflow options¶
| Option | Purpose |
|---|---|
-i, --experiment-dir |
experiment directory |
-g, --genome |
normalized assembly name |
-j, --mode |
auto, all, a range, or a comma-separated selection |
-m, --metadata |
tabular metadata whose first column is filename |
-T, --trim-tool |
skewer or fastp; default is Skewer |
-M, --map-tool |
RNA mapper: HISAT2, STAR, or the lab-specific, multimapping-permissive STAR-TE preset |
--dry-run |
validate and construct the DAG without submission |
--rerun-selected-steps |
delete and recompute selected stage outputs |
--site-config |
override the discovered user site configuration |
--retention-policy |
all, pruned, or minimal |
--max-project-size |
soft cap such as 300G or 800GB |
--keep-duplicates |
override assay default and retain duplicates |
--remove-duplicates |
override assay default and remove duplicates |
-X, --no-multiqc |
disable final MultiQC aggregation |
Metadata and DE options¶
| Option | Purpose |
|---|---|
--sample-name |
columns used to derive unique sample IDs; required whenever metadata is supplied |
--input-match |
ChIP input matching columns; requires role metadata, used in preparation and analytical control resolution |
-I, --input |
legacy single shared ChIP control BAM; cannot be combined with metadata roles |
--chip-regions-bed |
protected custom non-overlapping ChIP testing BED; bypasses joint discovery |
--chip-joint-peak-q |
permissive joint testing-region MACS q threshold; default 0.1 |
--chip-se-fragment-length |
inferred SE fragment extension for ChIP MACS calls; default 200 bp |
--chip-effective-genome-size |
effective size used consistently by ChIP MACS calls; default approximate total reference length |
--chip-input-tracks |
fold_enrichment (default), log2_ratio, qpois, or none; visualization only |
--sample-type |
columns used to group peaks and hubs |
--sample-color |
columns used to derive palette categories |
--de-columns |
biological variables in an automatic DE design |
--de-block |
blocking variables in an automatic DE design |
--de-interactions |
include the interaction of two DE columns |
--de-formula |
explicit formula overriding automatic design options |
--de-config |
repeatable DE analysis YAML |
--de-out-dir |
output subtree for one DE analysis |
See the assay pages for ATAC/ChIP peak and broad-mode options.