Cluster flag for snk
Kobie-Kirven opened this issue · comments
Hi @Wytamma, I have really enjoyed using snk! I was wondering if there is a way to specify the '--cluster' flag for Snakemake from the snk command line?
Best,
Kobie.
Hi @Kobie-Kirven!
You should be able to pass any additional snakemake cli to the Snk cli and they will be forwarded to snakemake e.g. workflow run --cluster qsub will run snakemake --cluster qsub … internally. If the snakemake flag clashes with your workflow cli I.e you have cluster: … in your config then you can prepend --snake to any flags you want to ensure get passed to snakemake e.g. workflow run --snake--cluster qsub.
let me know if you have any other issues. Glad that you’re enjoying snk :)
Hi @Wytamma, thank you for your reply! That's good to know about the flag forwarding and I got it working now. Thanks again!
Best,
Kobie.