Jorge Langa
Jorge Langa
I'll continue next week
@fgvieira I think I am done with this wrapper. I've left commented the part about outputting extra files from bowtie2 (metrics, unaligned, unpaired, concordant and unconcordant). Some of them introduce...
I don't understand. All my commits are on the `bowtie2_sort` branch. I have nothing else pending to push in my computer.
I clicked the Update Branch button. I hope it was that.
I see that we both removed the patch number, but in a comment later you appended the one for `picard-slim`: ``` - picard-slim =3.3.0 ``` Is that correct? That one...
Ok. I see other wrappers with picard-slim =3.3.0. Fixing that and repinning everything.
Ok. Pinned everything with the exception of samtools. The pin file stays the same after that.
My initial plan was to just do either samtools view or sort, but I saw the wrapper from [bwa-mem2](https://github.com/snakemake/snakemake-wrappers/blob/7b6aa5ce164a4f1c45716ae9c56dbe6d330c08f3/bio/bwa-mem2/mem/wrapper.py) and I saw that it could be done for sam, bam...
@bethanyj28 review please?
@jenniferlu717