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Vini2 / phables

🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes
https://phables.readthedocs.io/
MIT License
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DEV: fix for run_combine_cov; reentrancy fix for scan_phrogs #16

Closed beardymcjohnface closed 1 year ago

beardymcjohnface commented 1 year ago

Hey Vijini, I ran into a couple of errors which this should fix. I'm also having another issue. When run_phables doesn't find any phages it does not write the resolved_paths.fasta file, or the resolved_phages directory. This tells snakemake that the job failed when it actually finished technically without error. I didn't try to patch it because I didn't know how you wanted to handle that sort of situation. Something like initialising an empty file and removing the directory from outputs could work.

Vini2 commented 1 year ago

Hey Mike!

Thanks for these fixes. I haven't handled this case. I will fix this.