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maxplanck-ie / snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data
http://snakepipes.readthedocs.io
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filter_reads in DNAmapping pipeline doesnt do the filtering #1023

Open LeilyR opened 4 months ago

LeilyR commented 4 months ago

Hi, even though I set dedup and mapq and see the string in the filter_rules, filtered bams areln -s of the bam files. I had a quick look at the rule, but I could not easily spot an obvious issue there. Did you notice this before? I am using bwa-mem2 btw

LeilyR commented 4 months ago

OK I found the bug, it is coming from here Filtering is only defined for bowtie2 not others. I will fix it in my locally installed one. Shall I send you a PR too?

LeilyR commented 4 months ago

I reopened this, since it is actually a bug to be fixed. Noticed that I cannot set a label anymore :P so maybe one of you can take care of that.

katsikora commented 4 months ago

Hey Leily,

thanks for posting that issue. I've been mostly testing on bowtie2 which is the default aligner, but I agree we should fix that. I'm only aware that UMI deduplication only works for bowtie2 sofar, this is also to be fixed for other aligners.

Were you able to open a PR?