From 9d2c262510975ce37d5da1f4e61a126af2f5ecac Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Patrick=20H=C3=BCther?= <huether@imb-mainz.de>
Date: Fri, 27 Oct 2023 16:26:43 +0200
Subject: [PATCH] add imb.config

---
 .github/workflows/main.yml |  1 +
 README.md                  |  1 +
 conf/imb.config            | 30 ++++++++++++++++++++++++++++++
 docs/imb.md                | 15 +++++++++++++++
 nfcore_custom.config       |  1 +
 5 files changed, 48 insertions(+)
 create mode 100644 conf/imb.config
 create mode 100644 docs/imb.md

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 8adaa81e1..045a84962 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -76,6 +76,7 @@ jobs:
           - "hypatia"
           - "icr_davros"
           - "ifb_core"
+          - "imb"
           - "imperial"
           - "incliva"
           - "ipop_up"
diff --git a/README.md b/README.md
index da067ab15..27aee94d1 100644
--- a/README.md
+++ b/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)
diff --git a/conf/imb.config b/conf/imb.config
new file mode 100644
index 000000000..930e81e73
--- /dev/null
+++ b/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 (huether@imb-mainz.de)'
+    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' }
+}
diff --git a/docs/imb.md b/docs/imb.md
new file mode 100644
index 000000000..86670d072
--- /dev/null
+++ b/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.
+:::
diff --git a/nfcore_custom.config b/nfcore_custom.config
index b4bbdf491..4465b786c 100644
--- a/nfcore_custom.config
+++ b/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" }