-
## Problem
The current GA4GH TES executor wraps every TES task in a Snakemake command, essentially making them 1-step Snakemake workflows. While this design choice aligned with that of other execut…
-
Hi Johannes,
I am trying to implement the https://github.com/snakemake-workflows/dna-seq-gatk-variant-calling workflow for non-vertebrate (plant) genomes that are available through ensemblgenomes.or…
-
**Snakemake version**
8.20.5
**Describe the bug**
When using a fresh Conda environment with Mamba and Snakemake as currently provided by Conda-forge and bioconda, the `--use-conda` option to …
-
Add an extra section about how to run workflows on HPC:
- Can run from login node - the workflow software will submit jobs for us automatically
- Need to run it from a persistent session using `tm…
-
Is it possible to enable the log directory to be set to something other than a directory in `.snakemake`? For large workflows that submit many jobs, it would be nice to be able to write these to a scr…
-
**Is your feature request related to a problem? Please describe.**
I am using snakemake via the API from Python. I will be executing long running workflows at the command line where I would like to…
-
@jafors just pointed me to this workflow and your paper, @a-h-b. Very impressive workflow (and very cool logo!;).
He also remembered, that we recently had a lot of [dada2 wrappers](https://snakemak…
-
Greetings!
I have numerous workflows that are essentially a Snakefile with a minimal Python package wrapper to provide a robust command line interface and facilitate testing, deployment, etc. For a…
-
I'm trying to update my snakemake workflow to v8+
My nuisance so far is the following. I submit my workflows as a job in the login node from where snakemake with the executor do their thing. Proble…
-
In closing [this PR](https://github.com/ComputationalRadiationPhysics/picongpu/pull/5082#issuecomment-2343515776), I had a look at the Snakemake workflows [here](https://github.com/ComputationalRadiat…