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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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Rotary Hangs When No Contigs Pass Coverage Filter #199

Closed LeeBergstrand closed 1 week ago

LeeBergstrand commented 3 months ago

Problem Description

In certain situations with lousy input data, Rotary can determine that no contigs pass the coverage filter, causing checkpoint' split_circular_and_linear_contigs' to write no circular or linear contig lists. This, in turn, causes rule combine_circular_and_linear_contigs to fail because the function aggregate_contigs returns an empty input list. This, in turn, causes the command cat | seqtk seq -l 60 > {output} to run, as {input} is empty. This command has infinite run time.

Proposed Solution

Throw a Python exception when no contigs pass the coverage filter.

LeeBergstrand commented 3 months ago

Addressed by https://github.com/rotary-genomics/rotary/pull/200

LeeBergstrand commented 1 week ago

Addressed by https://github.com/rotary-genomics/rotary/pull/214