mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-12-04 20:49:54 +00:00
44 lines
1.7 KiB
Markdown
44 lines
1.7 KiB
Markdown
# nf-core/configs: IFB core Configuration
|
|
|
|
All nf-core pipelines have been successfully configured for use on the cluster of the IFB (Institut Francais de Bioinformatique).
|
|
|
|
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
|
|
|
|
Here is [the link to the cluster's documentation](https://ifb-elixirfr.gitlab.io/cluster/doc/quick-start/).
|
|
Before running the pipeline you will need to load Nextflow and other dependencies using the environment module system on IFB core. You can do this by issuing the commands below:
|
|
|
|
```bash
|
|
# Login to a compute node
|
|
srun --pty bash
|
|
|
|
## Load Nextflow and Singularity environment modules
|
|
module purge
|
|
module load nextflow
|
|
module load singularity
|
|
module load openjdk
|
|
|
|
|
|
# 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).
|