Update NCI Gadi config #920
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Included fixes from #872 |
pontus
reviewed
Jun 25, 2025
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| // Enable use of Singularity to run containers | ||
| singularity { | ||
| enabled = true | ||
| autoMounts = true | ||
| cacheDir = "/scratch/${params.project}/singularity" |
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Does this exist already, writable for everyone with the same project set?
| @@ -56,7 +74,18 @@ The version of Nextflow installed on Gadi has been modified to make it easier to | |||
| process { | |||
| executor = 'pbspro' | |||
| project = 'aa00' | |||
| storage = 'scratch/aa00+gdata/aa00' | |||
| storage = 'scratch/params.project' | |||
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I see there's apparently since before the "recommendation" to make a copy of the config file rather than just overriding what's needed (as typically done, e.g. as referenced from https://nf-co.re/docs/usage/getting_started/configuration).
If one does, this should have an expansion I assume? (Or could be hardcoded if a user does her own config).
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name: NCI Gadi HPC
about: added new instructions re: use of persistent sessions to docs, directed singularity cacheDir to
/scratchto avoid issues with defaulting to/homePlease follow these steps before submitting your PR:
[WIP]in its titlemasterbranchSteps for adding a new config profile:
conf/directorydocs/directorynfcore_custom.configfile in the top-level directoryprofile:scope in.github/workflows/main.yml.github/CODEOWNERS(**/<custom-profile>** @<github-username>)