Merge pull request #568 from dsloanm-uodit/master

Add University of Dundee cluster config

.github/workflows/main.yml

@@ -117,6 +117,7 @@ jobs:
           - "uge"
           - "unibe_ibu"
           - "unc_lccc"
+          - "uod_hpc"
           - "uppmax"
           - "utd_ganymede"
           - "utd_sysbio"

README.md

@@ -171,6 +171,7 @@ Currently documentation is available for the following systems:
 - [UNC_LCCC](docs/unc_lccc.md)
 - [UGE](docs/uge.md)
 - [UNIBE_IBU](docs/unibe_ibu.md)
+- [UOD_HPC](docs/uod_hpc.md)
 - [UPPMAX](docs/uppmax.md)
 - [UTD_GANYMEDE](docs/utd_ganymede.md)
 - [UTD_SYSBIO](docs/utd_sysbio.md)

conf/uod_hpc.config

@@ -0,0 +1,26 @@
+params {
+  config_profile_description = 'University of Dundee Compute Cluster'
+  config_profile_contact = 'Dominic Sloan-Murphy ([email protected])'
+  config_profile_url = 'https://uod-hpc.readthedocs.io/en/latest/software/nextflow/'
+}
+
+process {
+  executor = 'sge'
+  penv = 'smp'
+  queue = 'all.q'
+
+  // Workaround for:
+  // https://github.com/nextflow-io/nextflow/issues/2449
+  withName: '.*' { memory = null }
+  withName: '.*' { time = null }
+}
+
+executor {
+  max_memory = 128.GB
+  max_cpus = 28
+  max_time = 72.h
+}
+
+conda {
+  enabled = true
+}

docs/uod_hpc.md

@@ -0,0 +1,38 @@
+# nf-core/configs: Dundee Configuration
+
+The nf-core pipelines [rnaseq](https://nf-co.re/rnaseq) and [sarek](https://nf-co.re/sarek) have been successfully tested on the [University of Dundee compute cluster](https://uod-hpc.readthedocs.io/en/latest/).
+
+To use, run the pipeline with `-profile uod_hpc`. This will download and launch the [`uod_hpc.config`](../conf/uod_hpc.config) which has been pre-configured with a setup suitable for the Dundee cluster.
+
+## Using Nextflow on Dundee Cluster
+
+Before running the pipeline you will need to install and configure Nextflow. You can do this by issuing the commands below:
+
+```bash
+# Create a Bioconda environment and install Nextflow
+setup-miniconda-env /cluster/<group_name>/<your_directory>/nextflow-env
+source "/cluster/<group_name>/<your_directory>/nextflow-env/bin/activate"
+conda config --add channels defaults
+conda config --add channels bioconda
+conda config --add channels conda-forge
+conda config --set channel_priority strict
+conda install -c bioconda nextflow
+
+# Specify a cache directory in your /cluster space for conda environments
+export NXF_CONDA_CACHEDIR="/cluster/<group_name>/<your_directory>/nxf-conda-cachedir"
+```
+
+For convenience, append the `export NXF_CONDA_CACHEDIR` and conda activation commands to your `.bashrc` file to avoid having to run on each log-in:
+
+```bash
+echo export NXF_CONDA_CACHEDIR='"/cluster/<group_name>/<your_directory>/nxf-conda-cachedir"' >> ~/.bashrc
+echo source '"/cluster/<group_name>/<your_directory>/nextflow-env/bin/activate"' >> ~/.bashrc
+```
+
+:::note
+You will need an account to use the HPC cluster in order to run the pipeline. If in doubt raise a support request with University of Dundee service desk.
+:::
+
+:::note
+Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt raise a support request with University of Dundee service desk.
+:::

nfcore_custom.config

@@ -99,6 +99,7 @@ profiles {
     uge              { includeConfig "${params.custom_config_base}/conf/uge.config" }
     unc_lccc         { includeConfig "${params.custom_config_base}/conf/unc_lccc.config" }
     unibe_ibu        { includeConfig "${params.custom_config_base}/conf/unibe_ibu.config" }
+    uod_hpc          { includeConfig "${params.custom_config_base}/conf/uod_hpc.config" }
     uppmax           { includeConfig "${params.custom_config_base}/conf/uppmax.config" }
     utd_ganymede     { includeConfig "${params.custom_config_base}/conf/utd_ganymede.config" }
     utd_sysbio       { includeConfig "${params.custom_config_base}/conf/utd_sysbio.config" }