Use channel helper in Purge dups workflow

NBISweden / Earth-Biogenome-Project-pilot

Assembly and Annotation workflows for analysing data in the Earth Biogenome Project pilot project.

https://www.earthbiogenome.org/

GNU General Public License v3.0

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Use channel helper in Purge dups workflow #105

Closed mahesh-panchal closed 4 months ago

mahesh-panchal commented 4 months ago

Use helper function to make assembly record.

MartinPippel commented 4 months ago

I think theoretically that's a very good idea. But in practice I have also seen multiple bacterial assemblies with duplicated contigs, mostly due to a higher error rates in some regions causing "spurs" or bubbles. Would there be an option to "force" purging for assemblies with ploidy=1? I guess setting ploidy to 2 would cause many undesired side effects (e.g. GenomeScope, etc.)

mahesh-panchal commented 4 months ago

Nah, you're right about that. Having to set ploidy is not a good way to circumvent this. Better just to let the user turn the stage off manually for haploids if it's not desired. Perhaps later I'll integrate turning off the workflow for haploids instead.

mahesh-panchal commented 4 months ago

OK. Limiting this PR to using the channel helper