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genomic-medicine-sweden / jasen

Bacterial typing pipeline for clinical NGS data. Written in NextFlow, Python & Bash.
https://jasen.readthedocs.io/en/latest/
GNU General Public License v3.0
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Makefile species-specific installation #351

Open ryanjameskennedy opened 2 weeks ago

ryanjameskennedy commented 2 weeks ago

It would be nice that if you're only interested in analysing one species, that you can provide an arguement to only pull and setup files for a specific species i.e. make install saureus

samuell commented 2 weeks ago

Indeed, but that is in a way what we do already in e.g. in the CI workflow:

https://github.com/genomic-medicine-sweden/jasen/blob/master/.github/workflows/ci.yml#L66-L68

... only that right now one has to run two commands (We in essence are only running make update_databases && make staphylococcus_aureus_all), so one could sure add meta-rules to do all that is required for each individual species!