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NBISweden / GenErode

GitHub repository for GenErode, a Snakemake pipeline for the analysis of whole-genome sequencing data from historical and modern samples to study patterns of genome erosion.
GNU General Public License v3.0
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Issues with cookiecutter in UPPMAX #31

Closed jcchacond closed 1 year ago

jcchacond commented 1 year ago

Hello,

I'm trying to set up the slurm profile with cookiecutter (using the latest version of the pipeline v0.4.2), but the options look very different to what is described in GenErode's Wiki.

This is how it looks like:

2022-12-14

Apparently it is asking me to manually input all the configuration instead of retrieving it from the config/cluster.yaml.

I used cookiecutter earlier this year both in UPPMAX and another slurm-based cluster and it was working exactly as it is described in the Wiki. I'm not sure if the issue I'm finding now is related to recent changes in UPPMAX or in the Snakemake git profile.

Thanks in advance, I'd appreciate any suggestions on how to proceed in order to set up the Snakemake profile.

verku commented 1 year ago

The cookiecutter is continuously being updated and eventually the cluster.yaml file may not work with it anymore. I'll look into it and will let you know how to solve this.

verku commented 1 year ago

Thanks again for letting me know! The latest slurm profile is still compatible with the cluster.yaml file from the pipeline. I've updated the WIKI with how to set up the slurm profile accordingly: https://github.com/NBISweden/GenErode/wiki/2.-Requirements-&-pipeline-configuration