diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 09ccec31f..a6348d609 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -128,6 +128,7 @@ jobs: - "mssm" - "munin" - "nci_gadi" + - "newcastle" - "nu_genomics" - "nygc" - "nyu_hpc" diff --git a/conf/newcastle.config b/conf/newcastle.config new file mode 100644 index 000000000..17ec1e842 --- /dev/null +++ b/conf/newcastle.config @@ -0,0 +1,22 @@ +params { + config_profile_description = 'Newcastle HPC cluster profile' + config_profile_contact = 'Chris Wyatt (@chriswyatt1), Fernando Duarte (@FernandoDuarteF)' + config_profile_url = '' +} + +executor { + name = 'slurm' +} + +process { + scratch = true + errorStrategy = { task.exitStatus in [137, 140] ? 'retry' : 'finish' } + queue = 'defq' // maps to `#SBATCH -p defq` + clusterOptions = '--account=DESIM' // maps to `#SBATCH -A DESIM` +} + +singularity { + enabled = true + pullTimeout = '2 h' + autoMounts = true +} diff --git a/docs/newcastle.md b/docs/newcastle.md new file mode 100644 index 000000000..fd220a670 --- /dev/null +++ b/docs/newcastle.md @@ -0,0 +1,46 @@ +# nf-core/configs: Newcastle HPC Configuration + +Configuration for the Newcastle high performance computing (HPC) cluster. + +## Setup + +To install nextflow we first need to get the prequisite java from module avail: + +`module load Java/17.0.6` + +Then installing Nextflow using the standard install options: +https://www.nextflow.io/docs/latest/install.html + +`curl -s https://get.nextflow.io | bash` + +Make Nextflow executable: + +`chmod +x nextflow` + +Then move Nextflow into an executable path. For example: + +`mkdir -p $HOME/bin/` +`mv nextflow $HOME/bin/` + +To ensure this works every time you login to the cluster, put inside your `~/.bash_profile` the java install: + +`nano ~/.bash_profile` + +Then paste in the line for the java install: + +``` +#Java module add v17: +module load Java/17.0.6 +``` + +Exit nano with, control-X, then y to save, then enter to confirm + +## Run + +To use this profile, simply pass Nextflow the -profile newcastle flag eg. + +```bash +nextflow run nf-core/_pipeline_ -profile newcastle --outdir results +``` + +In case of issues, please feel free to reach out to one of the maintainers (Chris Wyatt or Fernando Duarte) at ecoflow.ucl@gmail.com . We are based at UCL, but helped set up this config, and are happy to help. diff --git a/nfcore_custom.config b/nfcore_custom.config index 229b06fa2..d7fdcb729 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -292,6 +292,9 @@ profiles { nci_gadi { includeConfig "${params.custom_config_base}/conf/nci_gadi.config" } + newcastle { + includeConfig "${params.custom_config_base}/conf/newcastle.config" + } nu_genomics { includeConfig "${params.custom_config_base}/conf/nu_genomics.config" }