Run entire Snakemake pipeline in a scratch space

Asked Jun 20 '19 at 17:23

Active Jun 20 '19 at 17:23

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I'm wondering if it's possible to run the entire Snakemake pipeline in a scratch space? I understand that the shadow directive allows one to run rules in isolated directories, but is it possible to do that for entire pipeline without having to write shadow for every rule?

Let me know if I'm missing something.

asked Jun 20 '19 at 17:23

Vivek Rai

One option could be to create a new directory in the scratch space, symlink in your input files and snakemake workflow, then execute snakemake from that directory. – Colin Jun 24 '19 at 08:36
Did you get this to work @Vivek Rai? – Al Bro Dec 10 '19 at 11:18
@AlBro I adopted Nextflow as primary tool.. and that made it easier. – Vivek Rai Mar 26 '20 at 19:54

Run entire Snakemake pipeline in a scratch space

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