snakemake-wrappers

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Cell Ranger wrapper

3

Hi Snakemake community! 👋 I'm developing a Snakemake workflow that uses 10x Genomics' Cell Ranger for preprocessing single-cell RNA-seq data, and I'd love to contribute a wrapper for [cellranger count](https://www.10xgenomics.com/support/software/cell-ranger-arc/latest/getting-started/what-is-cell-ranger-arc)...

mschecht

Hey everyone, I need to rerun some old workflows for new datasets. Due to the latest development all the anaconda channels are blocked globally on our HPC. These old wrappers...

gernophil

feat: Add mmseqs2 main workflows

1

### QC * [x] I confirm that I have followed the [documentation for contributing to `snakemake-wrappers`](https://snakemake-wrappers.readthedocs.io/en/stable/contributing.html). While the contributions guidelines are more extensive, please particularly ensure that: * [x] `test.py`...

fgvieira

The idea is to have a dictionary that keeps track of tool-defined file suffixes and `output: filename=`: https://github.com/snakemake/snakemake-wrappers/pull/3974/files#diff-fc2a3b28a6423504a3ad1b54913414d281d379e7245af9504d867e2586a11f9bR51-R65 This can then be used to systematically create move commands once the...

dlaehnemann

feat: bowtie2 can now sort with samtools and picard

15

This PR shamelessly copies functionalities from bwa-mem2 to sort or not, do it by coordinate or queryname, and choose between samtools and picard to do so ### QC * [x]...

jlanga