Merge pull request #43 from apeltzer/master

BINAC SMP / Short / Long Updates

conf/binac.config

@@ -13,13 +13,14 @@ 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 = 128.GB
+  max_memory = 1024.GB
   max_cpus = 28
-  max_time = 48.h
+  max_time = 168.h
 }
 
 weblog{

docs/pasteur.md

@@ -4,33 +4,35 @@ 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#)
 
+- 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/rnaseq/blob/master/docs/usage.md#--custom_config_base)
+4. Get the nf-core Pasteur profile: [here](https://github.com/nf-core/configs#offline-usage)
 5. Run nextflow on a compute node:
+
 ```bash
 # create a terminal
 tmux