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I setup my config file and I run snakemake --cores all --use-conda --configfile config_argania.yaml
here is the error :
Config file config/config.yaml is extended by additional config specified vi…
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Hi, I'd like to use your package but I'm having issues with installation. I've followed all the steps until:
`snakemake --use-conda --conda-create-envs-only --cores 1`
But I get the following e…
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I am currently trying to run MTase linker in v0.4.11. The snakemake commands are failing because spaces are introduced through the workflow. These spaces make all jobs fail.
Command ran:
```
nan…
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So I have tried the `import_lark` branch out (https://github.com/lark-parser/lark/pull/1446). I must admit, I am a complete beginner with Lark and so I'm not sure if my error is due to that, or due to…
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## Checklist
- [x] I am using the current [`main`](https://github.com/pypsa-meets-earth/pypsa-earth/tree/main) branch or the latest [release](https://github.com/pypsa-meets-earth/pypsa-earth/re…
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With Snakemake 7.32.4, I could have a SnakeFile like this where I reconfigured the log format of snakemake to be consistent with the log format used by the rest of my python code :
```python
imp…
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**Snakemake version**
8.16
**Describe the bug**
There are many cluster environments where you are not allowed to run snakemake from login nodes, and you have run snakemake in a SLURM …
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Hii
I have a Snakefile that extracts a list of SRR accession numbers and stores them in a CSV file. Subsequently, I have a rule for downloading these files, followed by a trimming rule, and other a…
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Hi,
I would like to start snakemake workflow using the Python API, not the command line. The use case is integration tests from within my pytest test suite. I could solve this by starting a subproce…
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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…