Update cambridge.md

docs/cambridge.md

@@ -5,10 +5,58 @@ 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 will need to install it into a directory you have write access to.
+Follow [these instructions](https://www.nextflow.io/docs/latest/getstarted.html#) from the Nextflow documentation.
+
+```
+# move to desired directory on HPC
+cd /home/<username>/path/to/dir
+# get the newest version
+wget -qO- https://get.nextflow.io | bash
+```
+
+### Obtain updated java version
+
+The java version on the HPC needs updating.
+
+```
+cd ~/
+wget https://download.oracle.com/java/20/latest/jdk-20_linux-x64_bin.tar.gz
+tar xvfz jdk-20_linux-x64_bin.tar.gz
+# add these lines to .bashrc
+export JAVA_HOME=/home/ef479/jdk-20.0.1
+export PATH=/home/ef479/jdk-20.0.1/bin:$PATH
+# Once above is done “java --version” should return:
+java --version
+java 20.0.1 2023-04-18
+```
+
+### Set up Singularity
+
+Singularity allows the use of containers. You also needs to make a directory to store Singularity cache.
+
+```
+module load singularity
+# make a directory for the cache
+mkdir -p /home/<username>/rds/hpc-work/path/to/cache/dir
+```
+
+### 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, the node and the cache directory for Singularity.
+
+```
+# create a working directory in rds/hpc-work
+mkdir /home/<username>/rds/hpc-work/dir/to/test
+cd /home/<username>/rds/hpc-work/dir/to/test
+
+# 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" --cacheDir "/home/<username>/rds/hpc-work/path/to/cache/dir" --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.