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| scratch = true | ||
| errorStrategy = { task.exitStatus in [137, 140] ? 'retry' : 'finish' } | ||
| queue = 'defq' // maps to `#SBATCH -p defq` | ||
| clusterOptions = '--account=DESIM' // maps to `#SBATCH -A DESIM` |
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Just to confirm, this works for every single user of the cluster?
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| process { | ||
| scratch = true | ||
| errorStrategy = { task.exitStatus in [137, 140] ? 'retry' : 'finish' } |
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This should already be in nf-core pipelines, but with an improved range: https://github.com/nf-core/tools/blob/75e643ad2c62cdc8ecd39aa56c0c314efd4b13e4/nf_core/pipeline-template/conf/base.config#L18
If you are adding this for non-official nf-core pipelines, I would recommend at least to match the nf-core one.
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| # nf-core/configs: Newcastle HPC Configuration | |||
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| Configuration for the Newcastle high performance computing (HPC) cluster. | |||
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Is this University of Newcastle?
| params { | ||
| config_profile_description = 'Newcastle HPC cluster profile' | ||
| config_profile_contact = 'Chris Wyatt (@chriswyatt1), Fernando Duarte (@FernandoDuarteF)' | ||
| config_profile_url = '' |
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Missing URL of cluster or instituteion
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You have no resource limits specified, are there no limits?
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Thanks James. We will speak to the HPC admins this week at Newcastle University (UK). To ensure all those issues are resolved. |
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name: New Config
about: A new cluster config
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 directoryprofile:scope in.github/workflows/main.yml.github/CODEOWNERS(**/<custom-profile>** @<github-username>)