add imb.config

.github/workflows/main.yml

@@ -76,6 +76,7 @@ jobs:
           - "hypatia"
           - "icr_davros"
           - "ifb_core"
+          - "imb"
           - "imperial"
           - "incliva"
           - "ipop_up"

README.md

@@ -134,6 +134,7 @@ Currently documentation is available for the following systems:
 - [ICR_DAVROS](docs/icr_davros.md)
 - [IFB](docs/ifb_core.md)
 - [IMPERIAL](docs/imperial.md)
+- [IMB](docs/imb.md)
 - [INCLIVA](docs/incliva.md)
 - [iPOP-UP](docs/ipop_up.md)
 - [Janelia Research Campus](docs/janelia.md)

conf/imb.config

@@ -0,0 +1,30 @@
+
+params {
+    config_profile_description = 'Institute of Molecular Biology (IMB) HPC cluster profile provided by nf-core/configs'
+    config_profile_url         = 'https://imb-mainz.de/'
+    config_profile_contact     = 'Patrick Hüther ([email protected])'
+    config_profile_name        = 'IMB HPC cluster'
+
+    max_cpus   = 32
+    max_memory = 1.TB
+    max_time   = 7.d
+}
+
+singularity {
+  enabled    = true
+  autoMounts = true
+}
+
+executor {
+    name      = 'slurm'
+    jobName   = { "${task.process.split(':').last()}" }
+    queueSize = 20
+}
+
+process {
+    scratch = '/jobdir/$SLURM_JOB_ID'
+    cache   = 'lenient'
+    queue   = "groups".execute().text.contains('imb-bioinfocf')
+            ? { task.time <= 5.h ? 'bcfshort' : 'bcflong' }
+            : { task.time <= 5.h ? 'short' : 'long' }
+}

docs/imb.md

@@ -0,0 +1,15 @@
+# nf-core/configs: IMB Configuration
+
+All nf-core pipelines have been successfully configured for use on the HPC system at the Institute of Molecular Biology (IMB) in Mainz / Germany.
+
+To use this profile, run the pipeline with `-profile imb`. This will download and launch the [`imb.config`](../conf/imb.config) which has been pre-configured with a setup suitable for the IMB HPC system. Using this profile, container images with all required software will be downloaded before execution of the pipeline.
+
+Before running the pipeline, you will need to load Nextflow using the environment module system on the IMB HPC system. You can do this by issuing the command below:
+
+```bash
+module load nextflow
+```
+
+:::note
+You will need an account to use the IMB HPC cluster in order to run the pipeline. If in doubt contact IT.
+:::

nfcore_custom.config

@@ -58,6 +58,7 @@ profiles {
     hypatia          { includeConfig "${params.custom_config_base}/conf/hypatia.config"}
     icr_davros       { includeConfig "${params.custom_config_base}/conf/icr_davros.config" }
     ifb_core         { includeConfig "${params.custom_config_base}/conf/ifb_core.config" }
+    imb              { includeConfig "${params.custom_config_base}/conf/imb.config" }
     imperial         { includeConfig "${params.custom_config_base}/conf/imperial.config" }
     incliva          { includeConfig "${params.custom_config_base}/conf/incliva.config" }
     ipop_up          { includeConfig "${params.custom_config_base}/conf/ipop_up.config" }