From 4e48d4cc62b8f4b7415867c2377534f0e9a17c74 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Tue, 30 Jul 2019 18:53:00 +0200
Subject: [PATCH] Fix remaining points by drpatelh

---
 README.md            |  4 ++--
 docs/pasteur.md      | 34 ++++++++++++++++++----------------
 nfcore_custom.config |  2 +-
 3 files changed, 21 insertions(+), 19 deletions(-)

diff --git a/README.md b/README.md
index af4aad1..5323165 100644
--- a/README.md
+++ b/README.md
@@ -83,8 +83,8 @@ See [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs
 Currently documentation is available for the following clusters:
 
 * [AQUILA](docs/aquila.md)
-* [BINAC](docs/binac.md)
 * [BIGPURPLE](docs/bigpurple.md)
+* [BINAC](docs/binac.md)
 * [CCGA](docs/ccga.md)
 * [CCGA_DX](/docs/ccga_dx.md)
 * [CFC](docs/binac.md)
@@ -98,8 +98,8 @@ Currently documentation is available for the following clusters:
 * [PRINCE](docs/prince.md)
 * [SHH](docs/shh.md)
 * [UCT_HEX](docs/uct_hex.md)
-* [UPPMAX-DEVEL](docs/uppmax-devel.md)
 * [UPPMAX](docs/uppmax.md)
+* [UPPMAX-DEVEL](docs/uppmax-devel.md)
 * [UZH](docs/uzh.md)
 
 ### Uploading to `nf-core/configs`
diff --git a/docs/pasteur.md b/docs/pasteur.md
index 554761b..6e2d825 100644
--- a/docs/pasteur.md
+++ b/docs/pasteur.md
@@ -4,36 +4,38 @@ 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)
-5. Run nextflow on a compute node:       
+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 
+tmux
 
 # Get a compute node
 salloc
@@ -46,7 +48,7 @@ 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  \\
diff --git a/nfcore_custom.config b/nfcore_custom.config
index 469d6af..69bb8f3 100644
--- a/nfcore_custom.config
+++ b/nfcore_custom.config
@@ -33,8 +33,8 @@ profiles {
   prince       { includeConfig "${params.custom_config_base}/conf/prince.config" }
   shh          { includeConfig "${params.custom_config_base}/conf/shh.config" }
   uct_hex      { includeConfig "${params.custom_config_base}/conf/uct_hex.config" }
-  uppmax_devel { includeConfig "${params.custom_config_base}/conf/uppmax.config"; includeConfig "${params.custom_config_base}/conf/uppmax-devel.config" }
   uppmax       { includeConfig "${params.custom_config_base}/conf/uppmax.config" }
+  uppmax_devel { includeConfig "${params.custom_config_base}/conf/uppmax.config"; includeConfig "${params.custom_config_base}/conf/uppmax-devel.config" }
   uzh          { includeConfig "${params.custom_config_base}/conf/uzh.config" }
 }