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nf-core / genomeqc

Compare the quality of multiple genomes, along with their annotations.
https://nf-co.re/genomeqc
MIT License
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Add test data #6

Closed chriswyatt1 closed 1 week ago

chriswyatt1 commented 3 weeks ago

We need a small test dataset for the whole pipeline, following nf-core guides.

I think this could be just two chromosomes (or parts of chromosomes that are orthologous). Could be super small, like 10000bp total. I am pretty sure all the code will work on tiny chromosomes.

chriswyatt1 commented 2 weeks ago

Hopefully done here: https://github.com/nf-core/test-datasets/pull/1339

Used just two mycoplasma genomes 2000 lines, and 300 lines of their gff files. Maybe a little too small, but working with gffread and orthofinder.

FernandoDuarteF commented 2 weeks ago

We should probably use the 4-field format, whether running with local files or RefSeq IDs

FernandoDuarteF commented 2 weeks ago

Solved and included in the test config. See nf-core/test-datasets#1343