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nf-configs/docs/ifb_core.md

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# nf-core/configs: IFB core Configuration
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All nf-core pipelines have been successfully configured for use on the cluster of the IFB (Institut Francais de Bioinformatique).
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To use, run the pipeline with `-profile ifb_core`. This will download and launch the [`ifb_core.config`](../conf/ifb_core.config) which has been pre-configured with a setup suitable for the IFB core cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
## How to use on IFB core
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Before running the pipeline you will need to load Nextflow using the environment module system on IFB core. You can do this by issuing the commands below:
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```bash
# Login to a compute node
srun --pty bash
## Load Nextflow and Singularity environment modules
module purge
module load nextflow/20.04.1
# Run a downloaded/git-cloned nextflow workflow from
nextflow run \\
nf-core/workflow \\
-resume
-profile ifb_core \\
--email my-email@example.org \\
-c my-specific.config
...
# Or use the nf-core client
nextflow run nf-core/rnaseq ...
```
## Databanks
A local copy of several genomes are available in `/shared/bank` directory. See
our [databank page](https://ifb-elixirfr.gitlab.io/cluster/doc/banks/)
to search for your favorite genome.
>NB: You will need an account to use the HPC cluster on IFB core in order to run the pipeline. If in doubt contact IT or go to [account page](https://my.cluster.france-bioinformatique.fr/manager2/login).