From 1f2786c78f24742f0cb719595efc0e275bc0a1c9 Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Wed, 16 Oct 2019 18:15:04 +0200
Subject: [PATCH 1/2] add genouest cluster

---
 README.md            |  1 +
 conf/genouest.config | 23 +++++++++++++++++++++++
 docs/genouest.md     | 36 ++++++++++++++++++++++++++++++++++++
 nfcore_custom.config |  2 ++
 4 files changed, 62 insertions(+)
 create mode 100644 conf/genouest.config
 create mode 100644 docs/genouest.md

diff --git a/README.md b/README.md
index 9a26324..451c12f 100644
--- a/README.md
+++ b/README.md
@@ -91,6 +91,7 @@ Currently documentation is available for the following clusters:
 * [CRICK](docs/crick.md)
 * [CZBIOHUB_AWS](docs/czbiohub.md)
 * [CZBIOHUB_AWS_HIGHPRIORITY](docs/czbiohub.md)
+* [GENOUEST](docs/genouest.md)
 * [GIS](docs/gis.md)
 * [HEBBE](docs/hebbe.md)
 * [KRAKEN](docs/kraken.md)
diff --git a/conf/genouest.config b/conf/genouest.config
new file mode 100644
index 0000000..68d82a6
--- /dev/null
+++ b/conf/genouest.config
@@ -0,0 +1,23 @@
+//Profile config names for nf-core/configs
+params {
+  config_profile_description = 'The GenOuest cluster profile'
+  config_profile_contact = 'Anthony Bretaudeau (@abretaud)'
+  config_profile_url = 'https://www.genouest.org'
+}
+
+singularity {
+  enabled = true
+  autoMounts = true
+  runOptions = '-B /scratch:/scratch -B /local:/local -B /db:/db'
+}
+
+process {
+  executor = 'slurm'
+}
+
+params {
+  igenomesIgnore = true
+  max_memory = 750.GB
+  max_cpus = 80
+  max_time = 336.h
+}
diff --git a/docs/genouest.md b/docs/genouest.md
new file mode 100644
index 0000000..9c37553
--- /dev/null
+++ b/docs/genouest.md
@@ -0,0 +1,36 @@
+# nf-core/configs: GenOuest Configuration
+
+All nf-core pipelines have been successfully configured for use on the GenOuest cluster.
+
+To use, run the pipeline with `-profile genouest`. This will download and launch the [`genouest.config`](../conf/genouest.config) which has been pre-configured with a setup suitable for the GenOuest 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.
+
+## Running the workflow on the GenOuest cluster
+
+Nextflow is installed on the GenOuest cluster. You need to activate it like this:
+
+```bash
+source /local/env/envnextflow-19.07.0.sh
+```
+
+Nextflow manages each process as a separate job that is submitted to the cluster by using the sbatch command.
+Nextflow shouldn't run directly on the submission node but on a compute node. Run nextflow from a compute node:
+
+```bash
+# Login to a compute node
+srun --pty bash
+
+# Load the dependencies if not done before
+source /local/env/envnextflow-19.07.0.sh
+
+# Run a downloaded/git-cloned nextflow workflow from
+nextflow run \\
+/path/to/nf-core/workflow \\
+-resume
+-profile genouest \\
+--email my-email@example.org  \\
+-c my-specific.config
+...
+
+# Or use the nf-core client
+nextflow run nf-core/rnaseq ...
+```
diff --git a/nfcore_custom.config b/nfcore_custom.config
index 6e320c4..06182f5 100644
--- a/nfcore_custom.config
+++ b/nfcore_custom.config
@@ -21,6 +21,7 @@ profiles {
   crick        { includeConfig "${params.custom_config_base}/conf/crick.config" }
   czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" }
   czbiohub_aws_highpriority { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config"; includeConfig "${params.custom_config_base}/conf/czbiohub_aws_highpriority.config" }
+  genouest     { includeConfig "${params.custom_config_base}/conf/genouest.config" }
   gis          { includeConfig "${params.custom_config_base}/conf/gis.config" }
   hebbe        { includeConfig "${params.custom_config_base}/conf/hebbe.config" }
   kraken       { includeConfig "${params.custom_config_base}/conf/kraken.config" }
@@ -43,6 +44,7 @@ params {
   // This is a groovy map, not a nextflow parameter set
   hostnames = [
     crick: ['.thecrick.org'],
+    genouest: ['.genouest.org'],
     uppmax: ['.uppmax.uu.se']
   ]
 }

From 883a761651739b9704b76b386523ee5eb0d072ed Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Wed, 16 Oct 2019 18:45:26 +0200
Subject: [PATCH 2/2] add link

---
 docs/genouest.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/docs/genouest.md b/docs/genouest.md
index 9c37553..85341ef 100644
--- a/docs/genouest.md
+++ b/docs/genouest.md
@@ -6,7 +6,9 @@ To use, run the pipeline with `-profile genouest`. This will download and launch
 
 ## Running the workflow on the GenOuest cluster
 
-Nextflow is installed on the GenOuest cluster. You need to activate it like this:
+Nextflow is installed on the GenOuest cluster. Some documentation is available on the [GenOuest website](https://www.genouest.org/howto/#nextflow).
+
+You need to activate it like this:
 
 ```bash
 source /local/env/envnextflow-19.07.0.sh