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44 lines
1.7 KiB
Markdown
44 lines
1.7 KiB
Markdown
# 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.
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## How to use on IFB core
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Here is [the link to the cluster's documentation](https://ifb-elixirfr.gitlab.io/cluster/doc/quick-start/).
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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:
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```bash
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# Login to a compute node
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srun --pty bash
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## Load Nextflow and Singularity environment modules
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module purge
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module load nextflow
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module load singularity
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module load openjdk
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# Run a downloaded/git-cloned nextflow workflow from
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nextflow run \\
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nf-core/workflow \\
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-resume
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-profile ifb_core \\
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--email my-email@example.org \\
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-c my-specific.config
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...
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# Or use the nf-core client
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nextflow run nf-core/rnaseq ...
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```
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## Databanks
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A local copy of several genomes are available in `/shared/bank` directory. See
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our [databank page](https://ifb-elixirfr.gitlab.io/cluster/doc/banks/)
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to search for your favorite genome.
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> 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).
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