Merge pull request #245 from ikeller/unibe_ibu

Unibe ibu

.github/workflows/main.yml

@@ -62,6 +62,7 @@ jobs:
             - 'sanger'
             - 'seg_globe'
             - 'uct_hpc'
+            - 'unibe_ibu'
             - 'uppmax'
             - 'utd_ganymede'
             - 'utd_sysbio'

README.md

@@ -125,6 +125,7 @@ Currently documentation is available for the following systems:
 * [SANGER](docs/sanger.md)
 * [SEG_GLOBE](docs/seg_globe.md)
 * [UCT_HPC](docs/uct_hpc.md)
+* [UNIBE_IBU](docs/unibe_ibu.md)
 * [UPPMAX](docs/uppmax.md)
 * [UTD_GANYMEDE](docs/utd_ganymede.md)
 * [UTD_SYSBIO](docs/utd_sysbio.md)

conf/unibe_ibu.config

@@ -0,0 +1,23 @@
+params {
+	config_profile_description = "University of Bern, Interfaculty Bioinformatics Unit cluster profile"
+	config_profile_contact = "irene.keller@dbmr.unibe.ch; info@bioinformatics.unibe.ch"
+	config_profile_url = "https://www.bioinformatics.unibe.ch/"
+	max_memory = 500.GB
+	max_cpus = 128
+	max_time = 240.h
+}
+
+process {
+	executor = "slurm"
+	maxRetries = 2
+	beforeScript = 'mkdir -p ./tmp/ && export TMPDIR=./tmp/'
+}
+
+executor {
+	queueSize = 30
+}
+
+singularity {
+	enabled = true
+	autoMounts = true
+}

docs/unibe_ibu.md

@@ -0,0 +1,5 @@
+# nf-core/configs: UNIBE_IBU Configuration
+
+Configuration file to run nf-core pipelines on the cluster of the [Interfaculty Bioinformatics Unit](https://www.bioinformatics.unibe.ch/) of the University of Bern.
+
+To use, run the pipeline with `-profile unibe_ibu`. This will download and launch the profile.config which has been pre-configured with a setup suitable for the IBU cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. **This requires a local installation of singularity**. It is easiest to submit the pipeline from a compute node. Once the image is cached, you can also submit from the login node.

nfcore_custom.config

@@ -56,6 +56,7 @@ profiles {
   sanger       { includeConfig "${params.custom_config_base}/conf/sanger.config"}
   seg_globe    { includeConfig "${params.custom_config_base}/conf/seg_globe.config"}
   uct_hpc      { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" }
+  unibe_ibu    { includeConfig "${params.custom_config_base}/conf/unibe_ibu.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" }