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Documentation update for the OIST configuration
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charles-plessy authored Sep 5, 2023
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Expand Up @@ -21,13 +21,19 @@ commands below:
```bash
## Load the latest Nextflow and Singularity environment modules
ml purge
ml bioinfo-ugrp-modules
ml Other/Nextflow
ml bioinfo-ugrp-modules Nextflow2

If you run a _nf-core_ pipeline via the `nf-core` tool, the following command
will load all the modules you need.

```bash
ml bioinfo-ugrp-modules nf-core
```

> NB: You will need an account to use the _Deigo_ cluster in order to run the
> pipeline. If in doubt contact IT.
> pipeline. If in doubt contact [SCDA](https://groups.oist.jp/scs/documentation).
>
> NB: Nextflow will submit the jobs via the SLURM scheduler to the HPC cluster
> and as such the commands above will have to be executed on one of the login
> nodes. If in doubt contact IT.
> NB: Nextflow submits the jobs via the SLURM scheduler to the compute nodes.
> You can run the `nextflow` or `nf-core` commands on the login nodes, but
> pay attention that the Nextflow `work` directory must be on the `/flash` file
> system.

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