Update cambridge.md

conf/cambridge.config

@@ -5,7 +5,6 @@ params {
   config_profile_url = "https://docs.hpc.cam.ac.uk/hpc"
   partition = null 
   project = null
-  cacheDir = null
   max_memory = 192.GB 
   max_cpus = 56
   max_time = 12.h 
@@ -15,7 +14,6 @@ params {
 singularity {
   enabled = true
   autoMounts = true
-  cacheDir = params.cacheDir
 } 
 
 process {

docs/cambridge.md

@@ -5,10 +5,79 @@ To use, run the pipeline with `-profile cambridge`. This will download and launc
 with a setup suitable for the Cambridge HPC cluster. Using this profile, either a docker image containing all of the required software will be downloaded,
 and converted to a Singularity image or a Singularity image downloaded directly before execution of the pipeline.
 
-The latest version of Nextflow is not installed by default on the Cambridge HPC cluster. You will need to install it into a directory you have write access to.
-Follow these instructions from the Nextflow documentation.
+### Install Nextflow
 
-- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#)
+The latest version of Nextflow is not installed by default on the Cambridge HPC cluster CSD3. You can install it with conda:
+
+```
+module load miniconda/3
+
+# set up Bioconda according to the Bioconda documentation, notably setting up channels
+conda config --add channels defaults
+conda config --add channels bioconda
+conda config --add channels conda-forge
+
+# create the environment env_nf, and install the tool nextflow
+conda create --name env_nf nextflow
+
+# activate the environment containing nextflow
+conda activate env_nf
+
+# once done with the environment, deactivate
+conda deactivate
+```
+
+Alternatively, you can install Nextflow into a directory you have write access to.
+Follow [these instructions](https://www.nextflow.io/docs/latest/getstarted.html#) from the Nextflow documentation. This alternative method requires also to update java.
+
+```
+# move to desired directory on HPC
+cd /home/<username>/path/to/dir
+
+# get the newest version
+wget -qO- https://get.nextflow.io | bash
+
+# update java version to the latest
+wget https://download.oracle.com/java/20/latest/jdk-20_linux-x64_bin.tar.gz
+tar xvfz jdk-20_linux-x64_bin.tar.gz
+
+# if all tools are compatible with the java version you chose, add these lines to .bashrc
+export JAVA_HOME=/home/<username>/path/to/dir/jdk-20.0.1
+export PATH=/home/<username>/path/to/dir/jdk-20.0.1/bin:$PATH
+
+# Once above is done `java --version` should return `java 20.0.1 2023-04-18`
+java --version
+
+```
+
+### Set up Singularity cache
+
+Singularity allows the use of containers and will use a caching strategy. First, you might want to set the `NXF_SINGULARITY_CACHEDIR` bash environment variable, pointing at your hpc-work location. If not, it will be automatically assigned to the current directory.
+
+```
+# do this once per login, or add these lines to .bashrc
+export NXF_SINGULARITY_CACHEDIR=/home/<username>/rds/hpc-work/path/to/cache/dir
+```
+
+Once done, and ready to use Nextflow, you can check that the Singularity module is loaded by default when logging on the cluster.
+
+```
+module list
+
+# If singularity is not loaded:
+module load singularity
+```
+
+### Run Nextflow
+
+Here is an example with the nf-core pipeline sarek ([read documentation here](https://nf-co.re/sarek/3.3.2)).
+The user includes the project name and the node.
+
+```
+# Launch the nf-core pipeline for a test database
+# with the Cambridge profile
+nextflow run nf-core/sarek -profile test,cambridge.config --partition "cclake" --project "NAME-SL3-CPU" --outdir nf-sarek-test
+```
 
 All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline
 has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway.