From 5348b8c609bac0b13003cc464f86ff6973ec1b95 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <apeltzer@users.noreply.github.com>
Date: Mon, 28 Oct 2019 13:12:31 +0100
Subject: [PATCH] Revert "BINAC SMP / Short / Long Updates"

---
 conf/binac.config |  5 ++---
 docs/pasteur.md   | 34 ++++++++++++++++------------------
 2 files changed, 18 insertions(+), 21 deletions(-)

diff --git a/conf/binac.config b/conf/binac.config
index e2bce86..9447ca4 100644
--- a/conf/binac.config
+++ b/conf/binac.config
@@ -13,14 +13,13 @@ process {
   beforeScript = 'module load devel/singularity/3.0.3'
   executor = 'pbs'
   queue = 'short'
-  process.queue = { task.memory > 128.GB ? 'smp': task.time <= 20m ? 'tiny' : task.time <= 48.h ? 'short' : task.time <= 168.h ? 'long'}
 }
 
 params {
   igenomes_base = '/nfsmounts/igenomes'
-  max_memory = 1024.GB
+  max_memory = 128.GB
   max_cpus = 28
-  max_time = 168.h
+  max_time = 48.h
 }
 
 weblog{
diff --git a/docs/pasteur.md b/docs/pasteur.md
index 6e2d825..554761b 100644
--- a/docs/pasteur.md
+++ b/docs/pasteur.md
@@ -4,38 +4,36 @@ All nf-core pipelines have been successfully configured for use on the tars clus
 
 To use, run the pipeline with `-profile pasteur`. This will download and launch the [`pasteur.config`](../conf/pasteur.config) which has been pre-configured with a setup suitable for the Pasteur 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 Pasteur cluster
 
 Nextflow is not installed by default on the Pasteur cluster.
-
 - Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#)
 
+
 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.
 The compute nodes don't have access to internet so you need to run it offline. 
 
 To do that:
-
 1. Create a virtualenv to install nf-core
-
-    ```bash
-    module purge
-    module load Python/3.6.0
-    module load java
-    module load singularity
-    cd /path/to/nf-core/workflows
-    virtualenv .venv -p python3
-    . .venv/bin/activate
-    ```
-
+```bash
+module purge
+module load Python/3.6.0
+module load java
+module load singularity
+cd /path/to/nf-core/workflows
+virtualenv .venv -p python3
+. .venv/bin/activate
+```
 2. Install nf-core: [here](https://nf-co.re/tools#installation)
 3. Get nf-core pipeline and container: [here](https://nf-co.re/tools#downloading-pipelines-for-offline-use)
-4. Get the nf-core Pasteur profile: [here](https://github.com/nf-core/configs#offline-usage)
-5. Run nextflow on a compute node:
-
+4. Get the nf-core Pasteur profile: [here](https://github.com/nf-core/rnaseq/blob/master/docs/usage.md#--custom_config_base)
+5. Run nextflow on a compute node:       
 ```bash
 # create a terminal
-tmux
+tmux 
 
 # Get a compute node
 salloc
@@ -48,7 +46,7 @@ module load singularity
 # Run nextflow workflow
 nextflow run \\
 /path/to/pipeline-dir/from/step/3/workflow \\
--resume
+-resume 
 -profile pasteur \\
 -with-singularity /path/to/pipeline-dir/from/step/3/singularity-images/singularity.img \\
 --email my-email@pasteur.fr  \\