Updated to roslin nf-core profile (Roslin Institute, University of Edinburgh) #943
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pontus
reviewed
Aug 15, 2025
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| The roslin profile is set to use `/exports/cmvm/eddie/eb/groups/alaw3_eb_singularity_cache` as the singularity cache directory. This directory is put at the disposition of roslin institute nextflow/nf-core users by the Roslin Bioinformatics group led by Andy Law. All new container will be cached in this directory writable by all. If you face any problem with singularity cache, please contact [Sébastien Guizard](sguizard@ed.ac.uk), [Donald Dunbar](donald.dunbar@ed.ac.uk) and [Andy Law](andy.law@roslin.ed.ac.uk) with the [Roslin Bioinformatics](roslin.bioinformatics@roslin.ed.ac.uk) group in CC. | ||
| We have now (from August 2025) configured the roslin profile to use apptainer rather than singularity in the worker node jobs. This works better for us on Eddie with Nextflow and the nf-core pipelines. The roslin profile is set to use `/exports/cmvm/eddie/eb/groups/alaw3_eb_singularity_cache` as the singularity cache directory. This directory is put at the disposition of roslin institute nextflow/nf-core users by the Roslin Bioinformatics group led by Andy Law. All new containers will be cached in this directory writable by all. If you face any problem with singularity cache, please contact [Sébastien Guizard](sguizard@ed.ac.uk), [Donald Dunbar](donald.dunbar@ed.ac.uk) and [Andy Law](andy.law@roslin.ed.ac.uk) with the [Roslin Bioinformatics](roslin.bioinformatics@roslin.ed.ac.uk) group in CC. |
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Having a globally writable directory means you trust all users equally to run code they create as you - and you make that choice for all users that don't actively investigate and change, if you have someone actually caring about this, it probably makes more sense to put that as a libraryDir (and restrict writing to a smaller group of trusted people).
pontus
reviewed
Aug 15, 2025
docs/roslin.md
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| nf-core pipelines sarek, rnaseq, chipseq, mag, differentialabundance and isoseq have all been tested on the University of Edinburgh Eddie HPC with test profile. | ||
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| ## Getting help | ||
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| There is a Teams group dedicated to Nextflow users: [Nextflow Teams](https://teams.microsoft.com/l/team/19%3A7e957d32ce1345b8989af14564547690%40thread.tacv2/conversations?groupId=446c509d-b8fd-466c-a66f-52122f0a2fcc&tenantId=2e9f06b0-1669-4589-8789-10a06934dc61) | ||
| Also, you can find at the coding club held each Wednesday: [Code Club Teams](https://teams.microsoft.com/l/channel/19%3A1bf9220112e445c382b6beb660ffb61a%40thread.tacv2/Coding%20Club?groupId=cc7a1113-38a1-48f6-9fc6-14700c8da27e&tenantId=2e9f06b0-1669-4589-8789-10a06934dc61) | ||
| Please also contact the Roslin Bioinformatics team with questions and we'll try to help: https://www.wiki.ed.ac.uk/spaces/RosBio/pages/602179073/Roslin+Bioinformatics+Home |
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Suggested change
| Please also contact the Roslin Bioinformatics team with questions and we'll try to help: https://www.wiki.ed.ac.uk/spaces/RosBio/pages/602179073/Roslin+Bioinformatics+Home | |
| Please also contact the Roslin Bioinformatics team with questions and we'll try to help: https://www.wiki.ed.ac.uk/spaces/RosBio/pages/602179073/Roslin+Bioinformatics+Home |
remove trailing whitespace
pontus
reviewed
Aug 15, 2025
docs/roslin.md
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| nf-core pipelines sarek, rnaseq, chipseq, mag, differentialabundance and isoseq have all been tested on the University of Edinburgh Eddie HPC with test profile. | ||
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| ## Getting help | ||
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| There is a Teams group dedicated to Nextflow users: [Nextflow Teams](https://teams.microsoft.com/l/team/19%3A7e957d32ce1345b8989af14564547690%40thread.tacv2/conversations?groupId=446c509d-b8fd-466c-a66f-52122f0a2fcc&tenantId=2e9f06b0-1669-4589-8789-10a06934dc61) | ||
| Also, you can find at the coding club held each Wednesday: [Code Club Teams](https://teams.microsoft.com/l/channel/19%3A1bf9220112e445c382b6beb660ffb61a%40thread.tacv2/Coding%20Club?groupId=cc7a1113-38a1-48f6-9fc6-14700c8da27e&tenantId=2e9f06b0-1669-4589-8789-10a06934dc61) | ||
| Please also contact the Roslin Bioinformatics team with questions and we'll try to help: https://www.wiki.ed.ac.uk/spaces/RosBio/pages/602179073/Roslin+Bioinformatics+Home | ||
| We also have some notes on running the rnaseq pipeline (and of course much applies to all nf-core pipelines) here: https://www.wiki.ed.ac.uk/spaces/RosBio/pages/649925054/Nextflow+and+nf-core |
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| We also have some notes on running the rnaseq pipeline (and of course much applies to all nf-core pipelines) here: https://www.wiki.ed.ac.uk/spaces/RosBio/pages/649925054/Nextflow+and+nf-core | |
| We also have some notes on running the rnaseq pipeline (and of course much applies to all nf-core pipelines) here: https://www.wiki.ed.ac.uk/spaces/RosBio/pages/649925054/Nextflow+and+nf-core |
remove trailing whitespace
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Hi @pontus I've ran prettier and it seems to have removed the white space (I didn't see it :0)
Hope it's fine now...
Thanks and all the best, Donald
pontus
approved these changes
Aug 15, 2025
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Thanks and all the best, Donald |
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name: New roslin Config
about: A new roslin 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>)