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nf-configs/docs/shh.md
James A. Fellows Yates e503a3a064
Added new cluster and singularity cache
2019-03-14 21:21:31 +01:00

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nf-core/configs: SHH Configuration

All nf-core pipelines have been successfully configured for use on the Department of Archaeogenetic's SDAG/CDAG clusters at the Max Planck Institute for the Science of Human History (MPI-SHH).

To use, run the pipeline with -profile shh. This will download and launch the shh.config which has been pre-configured with a setup suitable for the SDAG and CDAG clusters. 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. The image will currently be centrally stored here:

/projects1/singularity_scratch/cache/

however this will likely change to a read-only directory in the future that will be managed by IT.

Note that the configuration file is currently optimised for nf-core/eager. It will submit to the short queue but with a walltime of 2 hours.

NB: You will need an account and VPN access to use the cluster at MPI-SHH in order to run the pipeline. If in doubt contact IT.

NB: Nextflow will need to submit the jobs via SLURM to the clusters and as such the commands above will have to be executed on one of the head nodes. If in doubt contact IT.