From 6bb7c1a4223d776cca1bea8834909c2c9f971c5f Mon Sep 17 00:00:00 2001
From: Sarah Guinchard <sarah.guinchard@univ-lille.fr>
Date: Thu, 12 May 2022 10:55:00 +0200
Subject: [PATCH 1/3] Update config file with queue & correct ressources

---
 conf/ifb_core.config | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/conf/ifb_core.config b/conf/ifb_core.config
index 50a72f4..64b571a 100644
--- a/conf/ifb_core.config
+++ b/conf/ifb_core.config
@@ -2,7 +2,7 @@
 params {
   config_profile_description = 'The IFB core cluster profile'
   config_profile_contact = 'https://community.france-bioinformatique.fr'
-  config_profile_url = 'https://www.france-bioinformatique.fr/'
+  config_profile_url = 'https://ifb-elixirfr.gitlab.io/cluster/doc/cluster-desc/'
 }
 
 singularity {
@@ -13,12 +13,12 @@ singularity {
 
 process {
   executor = 'slurm'
+  queue = { task.time <= 24.h ? 'fast' : 'long' }
 }
 
 params {
   igenomes_ignore = true
-  // Max resources requested by a normal node on genotoul.
-  max_memory = 240.GB
-  max_cpus = 28
-  max_time = 96.h
+  max_memory = 252.GB
+  max_cpus = 56
+  max_time = 720.h
 }

From 84457cc6559f18d6664d346ca48a3b0306e82ccf Mon Sep 17 00:00:00 2001
From: Sarah Guinchard <sarah.guinchard@univ-lille.fr>
Date: Thu, 12 May 2022 11:01:36 +0200
Subject: [PATCH 2/3] Update documentation

---
 docs/ifb_core.md | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/docs/ifb_core.md b/docs/ifb_core.md
index b9eb978..caf588a 100644
--- a/docs/ifb_core.md
+++ b/docs/ifb_core.md
@@ -6,7 +6,8 @@ To use, run the pipeline with `-profile ifb_core`. This will download and launch
 
 ## How to use on IFB core
 
-Before running the pipeline you will need to load Nextflow using the environment module system on IFB core. You can do this by issuing the commands below:
+Here is [the link to the cluster's documentation](https://ifb-elixirfr.gitlab.io/cluster/doc/quick-start/).
+Before running the pipeline you will need to load Nextflow and other dependencies using the environment module system on IFB core. You can do this by issuing the commands below:
 
 ```bash
 # Login to a compute node
@@ -14,7 +15,10 @@ srun --pty bash
 
 ## Load Nextflow and Singularity environment modules
 module purge
-module load nextflow/20.04.1
+module load nextflow
+module load singularity
+module load openjdk
+
 
 # Run a downloaded/git-cloned nextflow workflow from
 nextflow run \\

From 3538f8511a2cb4d311fbd4a67bc3cc1fbd6788db Mon Sep 17 00:00:00 2001
From: Sarah Guinchard <sarah.guinchard@univ-lille.fr>
Date: Thu, 12 May 2022 11:02:42 +0200
Subject: [PATCH 3/3] removed comment

---
 conf/ifb_core.config | 1 -
 1 file changed, 1 deletion(-)

diff --git a/conf/ifb_core.config b/conf/ifb_core.config
index 64b571a..6331278 100644
--- a/conf/ifb_core.config
+++ b/conf/ifb_core.config
@@ -6,7 +6,6 @@ params {
 }
 
 singularity {
-  // need one image per execution
   enabled = true
   runOptions = '-B /shared'
 }