Fix circularize medaka missing contigs file

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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Fix circularize medaka missing contigs file #194

Closed LeeBergstrand closed 2 weeks ago

LeeBergstrand commented 2 weeks ago

Potentially fixes issue https://github.com/rotary-genomics/rotary/issues/193

LeeBergstrand commented 2 weeks ago

@jmtsuji When is medaka ran during the circularization process? Is it only ran on the circular contigs? Since the circular contig list only contains the circular contigs names it is identical to the contig manifest that medaka needs. So I take a copy and place that where the snakemake code is looking.