Run commands from a1_p1_qc/. Use Snakemake profiles for cores, conda, reruns, and module-local config overrides.
| Module | Main target | Runbook |
|---|---|---|
| fetch | fetch_all |
runbook_fetch.md |
| fastq_prepros | fastq_prepros_all |
runbook_fastq_prepros.md |
| standardize | standardize_all |
runbook_standardize.md |
| qc_preproc | qc_all |
runbook_qc_preproc.md |
| integration_annotation | integration_annotation_all |
runbook_integration_annotation.md |
Default profile:
snakemake --profile profiles/local -s <module>/Snakefile -n -p <target>Profile behavior and CPU/GPU presets are summarized in ../profiles/README.md.