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fmalmeida / MpGAP

Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads
https://mpgap.readthedocs.io/en/latest/
GNU General Public License v3.0
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should hifiasm be executed only when user says reads are high quality? #72

Closed fmalmeida closed 4 months ago

fmalmeida commented 4 months ago

The pipeline (in dev branch) now has two params:

--corrected_longreads and high_quality_longreads.

Maybe would be worthy to make hifiasm only run when one of these are available?

This is a follow up of #53

@scintilla9 any strong opinion?

fmalmeida commented 4 months ago

Currently, in the latest release, https://github.com/fmalmeida/MpGAP/releases/tag/v3.2.0, hifiasm is only executed if long reads are said to be corrected or high quality. Otherwise, not.

If a different behaviour is desired in the future, an issue should be opened.