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ctmrbio / stag-mwc

StaG Metagenomic Workflow Collaboration
https://stag-mwc.readthedocs.org
MIT License
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Make HUMAnN rules use resources.tmpdir directive instead of params.tmpdir #213

Closed boulund closed 1 year ago

boulund commented 1 year ago

The standard resource tmpdir is evaluated in the final execution context, making it more suited than simply referring to e.g. $TMPDIR, which may be evaluated in the wrong context when executing on a cluster.

https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#standard-resources

We should update the existing HUMAnN rules to use resources.tmpdir instead of our custom workaround.

boulund commented 1 year ago

Merged to develop, ready for release