From b48136a62e547aa2c8f337f76d4872ef4b80a224 Mon Sep 17 00:00:00 2001
From: ameynert <alison.meynert@igmm.ed.ac.uk>
Date: Thu, 18 Mar 2021 12:55:03 +0000
Subject: [PATCH] Added pipeline-specific config files

---
 docs/eddie.md | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/docs/eddie.md b/docs/eddie.md
index faecad7..5a8dfa5 100644
--- a/docs/eddie.md
+++ b/docs/eddie.md
@@ -14,7 +14,7 @@ This will download and launch the [`eddie.config`](../conf/eddie.config) which h
 The configuration file supports running nf-core pipelines with Docker containers running under Singularity by default. Conda is not currently supported.
 
 ```bash
-nextflow run nf-core/PIPELINE -profile eddie  # ..rest of pipeline flags
+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. 
@@ -33,6 +33,14 @@ module load igmm/apps/nextflow
 
 This config enables Nextflow to manage the pipeline jobs via the SGE job scheduler and using Singularity for software management.
 
+### Pipeline-specific config files
+
+In addition to the generic nf-core configuration accessed via `-profile eddie`, there are pipeline-specific configuration files in the NextGenResources fileset to handle processes that are known to require specific custom configuration on the eddie system, in particular Java processes which require an extra memory overhead. For example:
+
+```bash
+nextflow run nf-core/rnaseq -profile eddie -c /exports/igmm/eddie/NextGenResources/nextflow/conf/eddie.rnaseq.config # ...rest of pipeline flags
+```
+
 ## Singularity set-up
 
 Load Singularity from the module system and set the Singularity cache directory to the NextGenResources path for the pipeline and version you want to run. If this does not exist, please contact the [IGMM Data Manager](data.manager@igmm.ed.ac.uk) to have it added. You can add these lines to the file `$HOME/.bashrc`, or you can run these commands before you run an nf-core pipeline.