Storage and retention¶

Sequencing depth can make raw and intermediate data substantially larger than a sample count alone suggests. Omnomnomics provides explicit retention policies and a soft project-size guard.

Retention policies¶

Policy	Behavior
all	keep all outputs and intermediates
pruned	keep FASTQ and reusable downstream products; remove bulky upstream intermediates after successful use
minimal	keep FASTQ and only terminal outputs required by the requested branches

omnomnomics rna \
  -i EXPERIMENT \
  -g GRCh38 \
  --retention-policy pruned

Cleanup is stage-aware. trimmed_FASTQ/ is not eligible until lane merging has completed, and BAM/ is not eligible until filtered BAM creation has completed. Lightweight trim and mapper metrics are copied to run_logs/flow_qc_cache/ before their source directories are removed, preserving later reporting.

Soft size guard¶

omnomnomics rna \
  -i EXPERIMENT \
  -g GRCh38 \
  --retention-policy minimal \
  --max-project-size 300G

The guard measures project usage at storage checkpoints and attempts only safe cleanup. If essential FASTQs and filtered BAMs already exceed the cap, the run records a warning. Space-heavy BigWig/track-hub branches may be skipped while requested count-table work continues.

This is a soft workflow policy, not a reservation. It cannot prevent failures caused by another project consuming the same filesystem quota or by temporary job-local scratch exhaustion.