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Updated to roslin nf-core profile (Roslin Institute, University of Edinburgh) #943

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Sep 16, 2025
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Updated to roslin nf-core profile (Roslin Institute, University of Edinburgh) #943

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e17c76b
changing to apptainer instead of singularity
Aug 14, 2025
1993ad1
Update docs mentioning apptainer. Will add more soon.
donalddunbar Aug 14, 2025
d94d5c9
Updated the roslin config doc (roslin.md)
donalddunbar Aug 15, 2025
a3a40e8
Prettier run on docs/roslin.md
donalddunbar Aug 15, 2025
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4 changes: 2 additions & 2 deletions conf/roslin.config
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Original file line number Diff line number Diff line change
Expand Up @@ -34,11 +34,11 @@ process {
maxErrors = '-1'
maxRetries = 3

// Force singularity version 3 as version 4 cause FUSE/squashfs issues on Eddie
// Use apptainer module instead of singularity
beforeScript =
"""
. /etc/profile.d/modules.sh
module load igmm/apps/singularity/3
module load igmm/apps/apptainer/1.3.4
export SINGULARITY_TMPDIR="\$TMPDIR"
"""
}
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29 changes: 10 additions & 19 deletions docs/roslin.md
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@@ -1,11 +1,14 @@
# nf-core/configs: Roslin Configuration

This profile is similar to the 'eddie' profile managed by the IGC team, but focusssed towards eddie/nf-core users at Roslin.
nf-core pipelines sarek, rnaseq, chipseq, mag, differentialabundance and isoseq have all been tested on the University of Edinburgh Eddie HPC with test profile.

## Getting help

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

## Using the Roslin config profile

Expand All @@ -23,22 +26,22 @@ Before running the pipeline, you will need to load Nextflow from the module syst
To list versions:

```bash
module avail|grep nextflow
module avail -C Nextflow
```

To load the most recent version (08/08/2024):
To load the most recent version (15/08/2024):

```bash
module load igmm/bac/nextflow/24.04.2
module load roslin/nextflow/24.10.2
```

This config enables Nextflow to manage the pipeline jobs via the SGE job scheduler and using Singularity for software management.
This config enables Nextflow to manage the pipeline jobs via the SGE job scheduler and using Singularity / apptainer for software management.

## Singularity set up
## Singularity / apptainer set up

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).


Singularity will by default create a directory `.singularity` in your `$HOME` directory on eddie. Space on `$HOME` is very limited, so it is a good idea to create a directory somewhere else with more room and link the locations.
Singularity/apptainer will by default create a directory `.singularity` in your `$HOME` directory on eddie. Space on `$HOME` is very limited, so it is a good idea to create a directory somewhere else with more room and link the locations.

```bash
cd $HOME
Expand All @@ -58,13 +61,6 @@ If you wish, you place this variable declaration in your `.bashrc` file located

**NB:** This will work only with the roslin profile.

## Nodes exclusion

The roslin profile excludes some specific nodes.
The superdome node is reserved for special applications, and the access must be requested.
Eddie's nodes are being migrated to Rocky Linux 9 and some of them are already online. These are not fully set up yet and jobs have troubles to run on them.
Until those nodes are stable, we exclude them.

## Running Nextflow

### On a login node
Expand Down Expand Up @@ -103,8 +99,3 @@ screen -r <session_name>
Wild West node has relaxed restriction compared to regular nodes, which allows the execution of Nextflow.
The access to Wild West node must be requested to [Andy Law](andy.law@roslin.ed.ac.uk) and IS.
Similarly to the qlogin option, it is advised to run Nextflow within a screen session.

## Using iGenomes references

A local copy of the iGenomes resource has been made available on the Eddie HPC for those with access to `/exports/igmm/eddie/BioinformaticsResources` so you should be able to run the pipeline against any reference available in the `igenomes.config`.
You can do this by simply using the `--genome <GENOME_ID>` parameter.
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