snakepipes

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modify config file while singularity container

5

Hi! I would like to know if you could help me, i would like to run the pipeline on server but for several reasons i can't install it with conda...

MarineBergot

- [x] deprecate mode Gruen scRNAseq - [ ] remove mode Gruen functionality entirely - [ ] make ``--fromBAM`` work the same way between workflows - [ ] rename ``--skipVelocyto``...

katsikora

- [ ] check which organisms need update in e.g. ensemble version - [ ] add GRCz11 - [ ] check if software can be bumped in env yamls -...

katsikora

katsikora

Adding bwa-mem2?

1

Hi, I was wondering if you might add native support for `bwa-mem2` as that is available through `bioconda`. I added it to my installation, but I guess it would be...

jelber2

- [ ] add HiC QC plot - [ ] add HiC correlate plot - given sample sheet, run HiC correlate for replicates belonging to one condition - [ ]...

katsikora

fix #785

8

closes #785

vivekbhr

Arima enzymes for Hi-C

4

Hello :) Just a small merge request to add Arima Genomics double enzymes cut sites to the pipeline. Building of matrices with fixed binsize is working. I need to test...

gtrichard

rMats - summary

1

Include summary.py run after rMats invocation

WardDeb

cutntag peak calling

3

bamtobed and peak calling on bed files

LeilyR