diff --git a/docs/eddie.md b/docs/eddie.md new file mode 100644 index 0000000..e6a2f87 --- /dev/null +++ b/docs/eddie.md @@ -0,0 +1,49 @@ +# nf-core/configs: Eddie Configuration + +nf-core pipelines sarek, rnaseq, and atacseq have all been tested on the University of Edinburgh Eddie HPC. + +## Getting help + +There is a Slack channel dedicated to eddie users on the MRC IGMM Slack: [https://igmm.slack.com/channels/eddie3](https://igmm.slack.com/channels/eddie3) + +## Using the Eddie config profile + +To use, run the pipeline with `-profile eddie` (one hyphen). +This will download and launch the [`eddie.config`](../conf/eddie.config) which has been pre-configured with a setup suitable for the [University of Edinburgh Eddie HPC](https://www.ed.ac.uk/information-services/research-support/research-computing/ecdf/high-performance-computing). + +The configuration file supports running nf-core pipelines with either a Conda environment or Docker containers running under Singularity. + +```bash +nextflow run nf-core/PIPELINE -profile eddie # ..rest of pipeline flags +``` + +Before running the pipeline you will need to install Nextflow or load it from the module system. Generally the most recent version will be the one you want. + +To list versions: + +```bash +module avail igmm/apps/nextflow +``` + +To load the most recent version: +```bash +module load igmm/apps/nextflow +``` + + +This config enables Nextflow to manage the pipeline jobs via the SGE job scheduler and using Conda or Singularity for software management. + +To set up Nextflow on a login node ... TODO + +## Using iGenomes references + +A local copy of the iGenomes resource has been made available on the Eddie HPC so you should be able to run the pipeline against any reference available in the `igenomes.config`. +You can do this by simply using the `--genome ` parameter. + +## Adjusting maximum resources + +This config is set for IGMM standard nodes which have 32 cores and 384GB memory. If you are a non-IGMM user, please see the [ECDF specification](https://www.wiki.ed.ac.uk/display/ResearchServices/Memory+Specification) and adjust the `--clusterOptions` flag appropriately, e.g. + +```bash +--clusterOptions "-C mem256GB" --max_memory "256GB" +```