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CRG-CNAG / CalliNGS-NF

GATK RNA-Seq Variant Calling in Nextflow
Mozilla Public License 2.0
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suggest adding docker runOptions to nextflow.config #16

Closed jayoung closed 3 years ago

jayoung commented 4 years ago

hi there,

I'm looking at this after taking your nextflow class last week at Fred Hutch - thanks again for that: it was really helpful.

It might be good to add to the nextflow.config file something like this: docker { enabled = true runOptions = "-u \$(id -u):\$(id -g)" }

because I just ran the pipeline as is from github and now I have files in a work dir that I cannot delete!

Also enabling docker here would prevent us naive users from having to figure this issue out: https://github.com/CRG-CNAG/CalliNGS-NF/issues/9

thanks!

Janet

pditommaso commented 3 years ago

Makes sense! thanks for the tip. 👉 8572630.