Add custom sarek config

conf/pipeline/sarek/m3c.config

@@ -0,0 +1,16 @@
+// Profile config names for nf-core/configs
+
+params {
+    // Specific nf-core/configs params
+    config_profile_contact = 'Famke Bäuerle (@famosab)'
+    config_profile_description = 'nf-core/sarek M3C profile provided by nf-core/configs'
+}
+
+// Specific nf-core/sarek process configuration
+process {
+    // In nf-core/sarek the time is set to 32.h, that means all jobs are being sent to cpu3-long which is not needed and stalls the pipeline
+    // Therefore we set the time to 24.h and only processes with label `process_long` that need more time will be sent to cpu3-long
+    withLabel:process_high {
+        time   = { 24.h  * task.attempt }
+    }
+}

docs/pipeline/sarek/m3c.md

@@ -0,0 +1,19 @@
+# nf-core/configs: uppmax sarek specific configuration
+
+Extra specific configuration for sarek pipeline
+
+## Usage
+
+To use, run the pipeline with `-profile m3c`.
+
+This will download and launch the sarek specific [`m3c.config`](../../../conf/pipeline/sarek/m3c.config) which has been pre-configured with a setup suitable for m3cx clusters.
+
+Example: `nextflow run nf-core/sarek -profile m3c`
+
+## Sarek specific configurations for the M3 cluster
+
+Specific configurations for the M3 Cluster has been made for sarek.
+
+- Runtime for `process_high`:
+  In nf-core/sarek the time is set to `32.h`, that means all jobs are being sent to `cpu3-long` which is not needed and stalls the pipeline.
+  Therefore we set the time to `24.h` and only processes with label `process_long` that need more time will be sent to `cpu3-long`.

pipeline/sarek.config

@@ -15,9 +15,6 @@ profiles {
     cfc {
         includeConfig "${params.custom_config_base}/conf/pipeline/sarek/cfc.config"
     }
-    cfc_dev {
-        includeConfig "${params.custom_config_base}/conf/pipeline/sarek/cfc.config"
-    }
     eddie {
         includeConfig "${params.custom_config_base}/conf/pipeline/sarek/eddie.config"
     }
@@ -27,6 +24,9 @@ profiles {
     icr_davros {
         includeConfig "${params.custom_config_base}/conf/pipeline/sarek/icr_davros.config"
     }
+    m3c {
+        includeConfig "${params.custom_config_base}/conf/pipeline/sarek/m3c.config"
+    }
     munin {
         includeConfig "${params.custom_config_base}/conf/pipeline/sarek/munin.config"
     }