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nf-cmgg / germline

A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data
https://nf-cmgg.github.io/germline/
MIT License
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Don't merge callable BED files if multiple CRAMs were given, rather remake them with mosdepth #104

Closed nvnieuwk closed 1 year ago

nvnieuwk commented 1 year ago

Description of the bug

It would be better for merged CRAM files to automatically regenerate a new BED file with mosdepth instead of merging the original ones. (This is less channel logic and will have better results)

Command used and terminal output

No response

Relevant files

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System information

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matthdsm commented 1 year ago

I agree. I would even take this further, run mosdepth by default and drop the callable_bed input.

nvnieuwk commented 1 year ago

Fixed in #100