species-wise merge - Githubissues

kfuku52 / amalgkit

RNA-seq data amalgamation for a large-scale evolutionary transcriptomics

BSD 3-Clause "New" or "Revised" License

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species-wise merge #23

Closed kfuku52 closed 3 years ago

kfuku52 commented 3 years ago

merge should be done for each species but not implemented so currently.

Hego-CCTB commented 3 years ago

Yeah, currently it just uses everything in a given directory. Species wise merge will need metadata.tsv as input, but should be no problem.

kfuku52 commented 3 years ago

This will make it easier to handle the data in the curate step as it should be done species-wise. It would be nice to store the merge outputs in species-wise directories like work_dir/merge/GENUS_SPECIES/. Could you work on this?

kfuku52 commented 3 years ago

I think we had a conversation years ago on how amalgkit outputs should be structured. Do you still have the note I took? You can follow that.

Hego-CCTB commented 3 years ago

Amalgkit update 0.5.1.1:

amalgkit merge now organises output species-wise when metadata guided

https://github.com/kfuku52/amalgkit/commit/ff964bc39848f6c981242108e884764c4b54a3c1