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Currently, our managed runtimes come with Snakemake version 7 so our core pathogen workflows have been written to work with that.
Snakemake [version 8](https://github.com/snakemake/snakemake/releas…
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**Current behaviour**
Consider the following workflow example:
- `reana.yaml` content:
```yaml
inputs:
files:
- inputs.yaml
- Snakefile
parameters:
input: inputs.yaml
w…
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### Lesson Title
Snakemake for Bioinformatics
### Lesson Repository URL
https://github.com/carpentries-incubator/snakemake-novice-bioinformatics
### Lesson Website URL
https://carpentries-incubat…
gperu updated
4 months ago
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**Is your feature request related to a problem? Please describe.**
Current documentation shows small examples. Working on real large datasets varies in some ways and has specific needs:
- limiting Da…
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**Snakemake version**
8.4.2
**Describe the bug**
As of PR #1407 fixing issue #1398, `SNAKEMAKE_PROFILE` cannot be passed to cluster jobs. We frequently used this as a required env varia…
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**Is your feature request related to a problem? Please describe.**
Including additional tools in MMEDS should be simply a matter of defining inputs, outputs, and command calls. It is unclear whether …
cleme updated
4 months ago
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**Current version in GwasQcPipeline**
```
$ snakemake --version
6.15.5
```
**Latest version**: [v8.20.5](https://github.com/snakemake/snakemake/releases/tag/v8.20.5)
## Migration…
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Some workflows from snakemake-workflows seem to trigger formatting warnings, maybe caused by inconsistent snakefmt behavior. Let's investigate that here.
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Hello, I'm a graduated student studying bioinformatics in South Korea.
I'm trying to do detect extrachromosomal DNA (ecDNA) in nanopore long-read targeted sequencing data.
I followed the workflow …
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## 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…