Merge pull request #426 from Aratz/master

Update UPPMAX documentation

docs/uppmax.md

@@ -8,7 +8,16 @@ We have a Slack channel dedicated to UPPMAX users on the nf-core Slack: [https:/
 
 ## Using the UPPMAX config profile
 
-Before running the pipeline you will need to either install `Nextflow` or load it using the environment module system (this can be done with e.g. `module load bioinfo-tools Nextflow/<VERSION>` where `VERSION` is e.g. `20.10`).
+The recommended way to activate `Nextflow`, `nf-core`, and any pipeline
+available in `nf-core` on UPPMAX is to use the [module system](https://www.uppmax.uu.se/resources/software/module-system/):
+
+```bash
+# Log in to the desired cluster
+ssh <USER>@{rackham,miarka,bianca}.uppmax.uu.se
+
+# Activate the modules, you can also choose to use a specific version with e.g. `Nextflow/21.10`.
+module load bioinfo-tools Nextflow nf-core nf-core-pipelines
+```
 
 To use, run the pipeline with `-profile uppmax` (one hyphen).
 This will download and launch the [`uppmax.config`](../conf/uppmax.config) which has been pre-configured with a setup suitable for the UPPMAX servers.
@@ -94,20 +103,12 @@ Before running a nf-core pipeline on `bianca` you will first have to download th
 In this guide, we use `rackham` to download and transfer files to the `wharf` area, but it can also be done on your own computer.
 If you use `rackham` to download the pipeline and the singularity containers, we recommend using an interactive session (cf [interactive guide](https://www.uppmax.uu.se/support/faq/running-jobs-faq/how-can-i-run-interactively-on-a-compute-node/)), which is what we do in the following guide.
 
-### Download and install Nextflow
-
-You can use the `Nextflow` UPPMAX provided `module`, but if necessary, you can also download a more recent version.
-
-```bash
-# Connect to bianca
-$ ssh -A <USER>-<BIANCA_PROJECT>@bianca.uppmax.uu.se
-
-# See the available versions for the module
-module spider Nextflow
+It is recommended to activate `Nextflow`, `nf-core` and your `nf-core`
+pipeline through the module system (see **Using the UPPMAX config profile**
+above). In case you need a specific version of any of these tools you can
+follow the guide below.
 
-# Load a specific version of the Nextflow module
-module load bioinfo-tools Nextflow/<VERSION>`
-```
+### Download and install Nextflow
 
 ```bash
 # Connect to rackham
@@ -160,19 +161,6 @@ $ export NXF_SINGULARITY_CACHEDIR=/castor/project/proj_nobackup/singularity-imag
 
 ### Install nf-core tools
 
-You can use the `nf-core` UPPMAX provided `module`, but if necessary, you can also download a more recent version.
-
-```bash
-# Connect to rackham
-$ ssh -X <USER>@rackham.uppmax.uu.se
-
-# See the available versions for the module
-module spider nf-core
-
-# Load a specific version of the nf-core module
-module load bioinfo-tools nf-core/<VERSION>`
-```
-
 ```bash
 # Connect to rackham
 $ ssh -X <USER>@rackham.uppmax.uu.se
@@ -254,7 +242,7 @@ And then `nf-core/<PIPELINE>` can be used with:
 $ nextflow run ~/<PIPELINE> -profile uppmax --project <BIANCA_PROJECT> --genome <GENOME_ASSEMBLY> ...
 ```
 
-## Update a pipeline
+### Update a pipeline
 
 To update, repeat the same steps as for installing and update the link.