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E.g. `config[genome]` where `genome` is defined in `configfile` or in cmdline using `--config` argument. Warn only about first usage and consider defined downstream.
```
rule download_fa:
out…
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# Snakebids: Reproducible neuroimaging workflows as BIDS apps
***By Tristan Kuehn, Jason Kai, and Ali Khan, Western University***
### Preferred sessions: Emergent Session #2 or Emergent Session #5…
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Workflows in the TRS-Filer db are synced with what's on the Snakemake Workflow Catalog, i.e., only new workflows are added, updated workflows are updated, and those that are not available anymore are …
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Over yonder at https://github.com/dib-lab/portable-snakemake-workflows/, I am working on a snakemake workflow that runs sgc to build a catlas. I am receiving the following error. I have looked through…
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**Snakemake version**
8.13
**Describe the bug**
I'm using the `slurm` executor plugin to have Snakemake submit jobs to cluster on my behalf. In addition to this, I'm also using the `fs` plugi…
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### Checklist
- [X] I added a descriptive title
- [X] I searched open requests and couldn't find a duplicate
### What is the idea?
Currently `conda.gateways.subprocess` implements:
```python
sub…
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**Is your feature request related to a problem? Please describe.**
no problem per se, just a tool that *could* know all the variables needed for calculation
**Describe the solution you'd like**
…
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To improve reproducibility look into creating a container with the required software.
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I am having trouble successfully kicking off any commands after running through the *Quick Start* and *The Really Quick Copy-And-Paste Quick Start*. Specifically I have to following questions:
1) I…
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**Snakemake version**
6.5.0
**Describe the bug**
When importing local code in subdirectories within workflows included as modules, python looks in the wrong parent folder despite the contents…