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nf-core / genomeqc

Compare the quality of multiple genomes, along with their annotations.
https://nf-co.re/genomeqc
MIT License
1 stars 1 forks source link

Add ncbigenomedownload module #2

Closed FernandoDuarteF closed 2 weeks ago

FernandoDuarteF commented 3 weeks ago

The ncbigenomedownload module from nf-core requires a file with a list of accessions, and, therefore, needs a path as input. Excon, which I'm trying to mimic here, requires a value string as input.

To fix this problem, at least temporariIy, I added in modules/local/create_path.csv a module that creates one file per species which contains one single accession, which is then used as an input by ncbigenomedownload.

chriswyatt1 commented 2 weeks ago

Great, nice to see it running the first step:

https://github.com/Eco-Flow/genomeqc/pull/7