Workflow stages¶

Steps 1 through 9 are shared preprocessing and signal-track stages.

Step	Stage	Result
1	Trim reads	trimmed_FASTQ/
2	FastQC	fastqc_reports/
3	Align reads	lane-level files in BAM/
4	Merge technical lanes	sample-level BAMs in BAM/
5	Touch up BAMs	filtered BAMs in filtered_BAM/
6	Index BAMs	.bai files
7	Alignment QC	tabular and PDF/SVG summaries
8	Create BigWigs	BigWigs/
9	Build grouped track hubs	merged_hubs/

Step 5 runs samtools collate, fixmate, sort, markdup, and view. Duplicates are kept by default for RNA and removed by default for ATAC and ChIP. Use --keep-duplicates or --remove-duplicates to override the assay default.

RNA follow-up steps¶

Step	Stage
10	Track-hub completion boundary
11	Create count table
12	Differential expression

ATAC and ChIP follow-up steps¶

Step	Stage
10	Call peaks or construct assay features
11	Peak QC
12	Pre-DE peak analysis
13	Create count table
14	Differential chromatin analysis
15	Post-DE peak interpretation

These assay-specific step numbers are the stable user interface used by -j, the monitor, and the run logs. Omnomnomics maps them to the required Snakemake rules for each assay.

Selecting stages¶

-j auto and -j all select the full assay workflow. Ranges and comma- separated selections are accepted:

# Map only
omnomnomics rna -i EXPERIMENT -g GRCh38 -j 1-3

# Resume from lane merging through RNA counting
omnomnomics rna -i EXPERIMENT -g GRCh38 -j 4-11

# Skip track-hub generation
omnomnomics rna -i EXPERIMENT -g GRCh38 -j 1-8,11-12

Every selected step must either receive an existing valid input or have that input produced by another selected/dependency step. Prefer contiguous ranges unless you understand the relevant file contracts.