filter_reads in DNAmapping pipeline doesnt do the filtering

[LeilyR]

Hi,
even though I set dedup and mapq and see the string in the filter_rules, filtered bams are ln -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]

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]

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]

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?