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Eco-Flow / comparete

A pipeline to compare TE content across genomes
MIT License
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Change logic to allow genomes without GFFs #3

Closed chriswyatt1 closed 2 months ago

chriswyatt1 commented 2 months ago

Currently you have to provide a ID, Refseq ID or ID, genome, gff. We may have species without gff from NCBI or your local files.

Also, we use the GFFREAD module to pull out the ID,Genome for TE classification, this should be done by a channel manipulation instead

chriswyatt1 commented 2 months ago

Fixed in f2996e3

Now you can enter species,genome.fa only - though genome must have the following endings for it to be recognised:

def fastaExtensions = ['.fa', '.fasta', '.fna', '.fa.gz', '.fasta.gz', '.fna.gz']