Differences

This shows you the differences between two versions of the page.

--- guides:slurm:nextflow [08.03.2024 14:53]
Administrator created
+++ guides:slurm:nextflow [27.09.2024 12:12] (current)
Administrator
@@ Line 1: / Line 1: @@
 # Example Nextflow config for SLURM
-//Profile config names for nf-core/configs
-params {
+Following example can be used as a [nextflow.config](https://www.nextflow.io/docs/latest/config.html) file.
-  config_profile_description = 'The University of Eastern Finland SLURM cluster profile'
-  config_profile_contact = 'Oskari Timonen'
-  config_profile_url = ''
-}
+    params {
+      config_profile_description = 'The University of Eastern Finland SLURM cluster profile'
-singularity {
+      config_profile_contact = 'Oskari Timonen'
-  enabled = true
+      config_profile_url = ''
-  autoMounts = true
+    }
-  cacheDir = "/some/fast/directory/for/apptainer/containers"
-}
+    singularity {
+      enabled = true
-process {
+      autoMounts = true
-  executor = 'slurm'
+      cacheDir = "/some/fast/directory/for/apptainer/containers"
+    }
-  queue = 'serial'
-  queueSize = 16
+    process {
+      executor = 'slurm'
-//  submitRateLimit = '20/2min'
-//  submitRateLimit = '1min'
+      queue = 'small'
-  maxSubmitJobs = 20
+      queueSize = 16
-  errorStrategy = 'retry'
+    //  submitRateLimit = '20/2min'
-  maxRetries = 5
+    //  submitRateLimit = '1min'
-  retry.delay = '1min'
+      maxSubmitJobs = 20
-// max 3.d on serial queue
+      errorStrategy = 'retry'
-  time = '1.d'
+      maxRetries = 5
-  cpus = 8
+      retry.delay = '1min'
-  memory = '50 GB'
+      time = '1.d'
-  clusterOptions = '--job-name=nfSLURM \
+      cpus = 8
-	--output=/directory/for/slurm/outputs/2024-03-08_output.txt \
+      memory = '20 GB'
-	--error=/directory/for/slurm/error/outputs/2023-03-08_log-error.txt \
-}
+      clusterOptions = '--job-name=nfSLURM \
+    	--output=/directory/for/slurm/outputs/2024-03-08_output.txt \
-params {
+    	--error=/directory/for/slurm/error/outputs/2024-03-08_log-error.txt \
-//  igenomes_ignore = true
+    }
-  max_memory = 100.GB
-  max_cpus = 32
+    params {
-  max_time = 3.d
+      max_memory = 50.GB
-}
+      max_cpus = 32
+      max_time = 3.d
+    }

Bioinformatics Center

User Tools

Site Tools

Differences

Page Tools