With a small --query input, most likely only a few strains need to be updated. It's not straightforward to support this as the top level jobs will rewrite all of the strain lists. This will require slightly more manual effort to support.
What I could do is:
- In the update script, do all of the processing that split strains and group stragglers normally do, manually.
- If only the new strain names and rfiles are updated, the snakemake file should then be possible to rerun
- but
included_samples would need more care, so that ska_index is just run on the new samples
Leaving this for now, as it feels like something that would only become worthwhile if actually requested.
With a small
--queryinput, most likely only a few strains need to be updated. It's not straightforward to support this as the top level jobs will rewrite all of the strain lists. This will require slightly more manual effort to support.What I could do is:
included_sampleswould need more care, so thatska_indexis just run on the new samplesLeaving this for now, as it feels like something that would only become worthwhile if actually requested.