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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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Allow long read-only with when polish_with_short_reads set to 'False'. #118

Closed LeeBergstrand closed 3 months ago

LeeBergstrand commented 5 months ago

I can do long read-only right now, but I have to make two fake Illumina files and turn the short read polish flag in the config to False.

We can modify the rule rule set_up_sample_directories: with some config-dependent switching logic and not need the short reads. This would be the low-hanging fruit.

_Originally posted by @LeeBergstrand in https://github.com/rotary-genomics/rotary/pull/114#discussion_r1484858455_

LeeBergstrand commented 5 months ago

@jmtsuji rule summarize_contigs_by_coverage in polish.smk fails when there is no short reads.

LeeBergstrand commented 5 months ago

It refers to both long and short rules in the same rule.

LeeBergstrand commented 3 months ago

@jmtsuji Fixed by https://github.com/rotary-genomics/rotary/pull/146