Comments (3)
Hi @J-Wall,
sure, that sounds useful! This week I'm quite busy, but I'll try to work on it next week!
So long
Lucas
from grenepipe.
Thanks @lczech ! No pressure :) I've hacked it together for myself, but without any testing etc..
from grenepipe.
Hi @J-Wall,
just added bwa-mem2 in the latest commit, thank you very much for your suggestion!
I took the code from your fork as inspiration (thank you very much!), but had to adapt the prep step (indexing) in your code, as this created file conflicts. Your code probably only works if the normal bwa index
was executed in a previous run of the pipeline, and then in a later run the bwa-mem2 index
is executed. The issue that I had is that the latter also creates amb
, ann
, and pac
files for the genome, which are identical with the original ones from bwa index
, but in the process of creating them twice, chaos ensued... I also fixed some issues in the actual mapping rule, such as taking the config file into account.
So, if your code is working for you at the moment, you can probably keep it. But for future-proofness of your fork, you might want to back-port my changes to yours as well.
Also, I'll be working on issue #8 soon. I hope to be able to use your code again as inspiration for this as well - thank you again!
Cheers
Lucas
from grenepipe.
Related Issues (20)
- Picard environment not created HOT 8
- snpEff download directory only works with a trailing slash HOT 3
- feature request: pass local reference genome database to snpEff HOT 2
- Updating run with new reads HOT 12
- support for haploid genomes? HOT 8
- Error in picard_collectmultiplemetrics HOT 4
- freebayes causes early error about number of threads HOT 12
- Call variants being rerun when adding new samples HOT 3
- Change link in wiki HOT 1
- BaseRecalibrator error - needs more readgroup info? HOT 2
- Error while running example HOT 6
- CondaMemoryError when creating conda envs in cluster HOT 3
- Run snakemake on Cluster HOT 3
- Conda installation error HOT 7
- Versions specified in conda env files and snakemake wrappers lead to conflicts/are not available HOT 11
- config file error HOT 5
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- bwa-mem2 "{tmp}.0000.bam": File exists HOT 5
- threads for bwa-mem2 via slurm HOT 2
- Error running toy example HOT 6
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