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Turning off --cpg option in Modkit via Human Variation pipeline #195

Open hassebossenbroek opened 4 days ago

hassebossenbroek commented 4 days ago

Ask away!

Hi, I have some bam files with modified base calls in any genomic context (5mC and 5hmC as opposed to 5mCG and 5hmCG). To analyse these, I'm trying to use the wf-human-variation, but I want to turn off the --cpg argument that gets passed to Modkit by default. I know that I can use --modkit_args to specify arguments to modkit, but it's not entirely clear to me how this works. The modkit pileup documentation seems to suggest --cpg is not a TRUE/FALSE argument, suggesting I can't just use --modkit_args --cpg FALSE. So my question is: If I pass --combine-strands as the only argument to --modkit_args, will the pipeline assume that the --cpg argument is no longer there and therefore look at the whole genome? Many thanks!

ArtRand commented 4 days ago

I've posted a workaround on modkit#221, but it might be worth making this flag optional.