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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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Rerun issue with snakemake 7.8 #32

Closed lored322 closed 1 year ago

lored322 commented 1 year ago

Many of us are now running GenErode with snakemake 7 to avoid issues with Singularity version changes. However, Snakemake has changed their rerun behaviour in Snakemake 7.8 (see https://github.com/snakemake/snakemake/issues/1694). This means that when changing metadata tables for example, snakemake will run everything from the beginning, stating "Set of input files has changed since last execution". To get around this you can use "--rerun-triggers mtime" in the snakemake command. Also applies to any local changes in code or other parameters.

verku commented 1 year ago

Thanks for looking into this! I'll make sure to update the documentation accordingly.

verku commented 1 year ago

The Wiki is now updated accordingly: https://github.com/NBISweden/GenErode/wiki/2.-Requirements-&-pipeline-configuration#1-prepare-metadata-files-of-samples