New config profile KAUST #809
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conf/kaust.config
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| // Keep work directory after a successful run | ||
| cleanup = false |
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Be wary of this, if users don't clean up their work directories manually and regularly, you may have very filled up hard drives very quickly
Nf-core pipelines come with a debug profile that can turn this off if necessary
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thanks for the note, I have now removed this flag. I thought to keep the decision to the user!
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It's better to keep it,= true actually,
Default is set to false!
conf/kaust.config
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| // Use existing images from the centralized library, if available | ||
| libraryDir = "/biocorelab/BIX/resources/singularity/images/" | ||
| // Download images that are missing from the library to user space | ||
| cacheDir = "/home/$USER/.singularity/nf_images/" |
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Please double check this works and nextflow doesn't try to resolve the variable [rather than bash] (this can happen in some of the config sections)
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And does the cache directory already exist for all users?
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I have already tested this and it works :)
yes, it will automatically create the cache directory if it doesn't exist
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Sorry @husensofteng I didn't see you were waiting for test execution approval. So you don't need to wait next time, feel free to join the nf-core GitHub org as described on https://nf-co.re/join |
thank you, I just sent a request! |
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| // Load genome resources and assets hosted by the Bioinformatics team on IBEX cluster | ||
| includeConfig '/biocorelab/BIX/resources/configs/genomes.yaml' |
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@jfy133 the profile does not recognize this statement, do you you have any suggestion how to make it work?
The purpose is to host a custom set of genome resources (similar to igenomes but locally maintained).
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I think users would have to specify it with a custom config i.e. with -c... @maxulysse any ideas?
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Unfortauntely this is breaking other pipeliens, so I'm commenting it out ofr now here: #810
name: New Config for KAUST
about: A new cluster config for KAUST Ibex cluster
Please 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 directoryREADME.mdfile in the top-level directoryprofile:scope in.github/workflows/main.yml.github/CODEOWNERS(**/<custom-profile>** @<github-username>)The purpose of this new config is to help users on the KAUST Ibex cluster to run nf-core workflows smoothly.
Thank you!