Short read improvements

rotary-genomics / rotary

Assembly/annotation workflow for Nanopore-based microbial genome data containing circular DNA elements

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

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Short read improvements #82

Closed LeeBergstrand closed 9 months ago

LeeBergstrand commented 9 months ago

removed perform_contaminant_filtration config parameter. Users can now leave both lists empty to skip filtering.
removed get_contamination_reference_file_paths as it is no longer necessary.
add code for symlinking custom file paths to the database directory.

LeeBergstrand commented 9 months ago

@jmtsuji This simplifies a bunch of your code. Thoughts? Note I have only '-dry-run' tested this.

LeeBergstrand commented 9 months ago

@LeeBergstrand Nice idea to simplify the contamination filter code. I left some comments, mostly about handling gzipped vs. non-gzipped custom FastA files and the need to have comma-separated input into the bbduk ref argument. Mind taking a look? Thanks!

I think this is already handled. See my comments to https://github.com/jmtsuji/rotary/pull/82#discussion_r1391874866

LeeBergstrand commented 9 months ago

@jmtsuji It passes my tests and makes it past the poly polish stage. If you think the gzip issues are addressed we should be good to merge.