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docs/eddie.md

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+# 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 <GENOME_ID>` 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"
+```