Added institutional configuration for shu_bmrc

.github/workflows/main.yml

@@ -132,8 +132,9 @@ jobs:
           - "sanger"
           - "scw"
           - "seawulf"
-          - "self_hosted_runner"
           - "seg_globe"
+          - "self_hosted_runner"
+          - "shu_bmrc"
           - "software_license"
           - "stjude"
           - "tes"

README.md

@@ -184,6 +184,7 @@ Currently documentation is available for the following systems:
 - [SEAWULF](docs/seawulf.md)
 - [SEG_GLOBE](docs/seg_globe.md)
 - [self-hosted-runner](docs/self-hosted-runner.md)
+- [SHU_BMRC](docs/shu_bmrc.md)
 - [StJude](docs/stjude.md)
 - [Super Computing Wales](docs/scw.md)
 - [GA4GH TES](docs/tes.md)

conf/shu_bmrc.config

@@ -0,0 +1,59 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Nextflow config file for Sheffield Hallam University BMRC Cluster
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Author: Dr Lewis A Quayle
+Mail: [email protected]
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+
+// params scope - displayed in header summary of each run
+
+params {
+
+  config_profile_description = 'Sheffield Hallam Universty - BMRC HPC'
+  config_profile_contact = 'Dr Lewis A Quayle ([email protected])'
+  config_profile_url = 'https://openflighthpc.org/latest/docs/'
+
+}
+
+
+// process scope - hpc configuration and auto-retry
+
+process {
+
+  resourceLimits = [
+    cpus: 64,
+    memory: 1007.GB,
+    time: 999.h
+  ]
+  executor = 'slurm'
+  maxRetries = 2
+
+}
+
+
+// executor scope - scheduler settings
+
+executor {
+
+  queueSize = 50
+  submitRateLimit = '1 sec'
+
+}
+
+
+// container scope
+
+apptainer {
+
+  enabled = true
+  autoMounts = true
+
+}
+
+
+// automatically delete intermediate work directory on successful completion of a run
+
+cleanup = true

docs/shu_bmrc.md

@@ -0,0 +1,13 @@
+# nf-core/configs: Sheffield Hallam University BMRC Cluster Configuration
+
+## Using the Institutional Configuration Profile
+
+To use [`shu_bmrc.config`](../conf/shu_bmrc.config), run nextflow with an nf-core pipeline using `-profile shu_bmrc` (note the single hyphen).
+
+This will download and launch [`shu_bmrc.config`](../conf/shu_bmrc.config) which has been pre-configured with a setup suitable for the BMRC cluster and will automatically load the appropriate pipeline-specific configuration file.
+
+## Running nf-core Pipelines on the BMRC Cluster
+
+A detailed guide to setting up Nextflow and nf-core and running pipelines on the BMRC Cluster is available here: [Running Nextflow with nf-core Pipelines on SHU BMRC Cluster](https://github.com/lquayle88/nfcore_on_shu_bmrc)
+
+If you have any questions or issues not addressed by this guide, please contact: [[email protected]](mailto:[email protected])

nfcore_custom.config

@@ -313,6 +313,9 @@ profiles {
     self_hosted_runner {
         includeConfig "${params.custom_config_base}/conf/self_hosted_runner.config"
     }
+    shu_bmrc {
+        includeConfig "${params.custom_config_base}/conf/shu_bmrc.config"
+    }
     software_license {
         includeConfig "${params.custom_config_base}/conf/software_license.config"
     }