Merge pull request #339 from jfy133/rnaseq_mpcdf

Add RNASEQ specific config for MPCDF

conf/mpcdf.config

@@ -32,7 +32,7 @@ profiles {
         params {
             config_profile_description = 'MPCDF cobra profile (unofficially) provided by nf-core/configs.'
             max_memory = 725.GB
-            max_cpus = 80
+            max_cpus = 40
             max_time = 24.h
         }
     }
@@ -47,7 +47,7 @@ profiles {
         }
        
         executor {
-            queueSize = 8
+            queueSize = 30
             pollInterval = '1 min'
             queueStatInterval = '5 min'
         }
@@ -61,7 +61,7 @@ profiles {
        
         params {
             config_profile_description = 'MPCDF raven profile (unofficially) provided by nf-core/configs.'
-            max_memory = 368.GB
+            memory = 2000000.MB
             max_cpus = 72
             max_time = 24.h
         }

conf/pipeline/eager/mpcdf.config

@@ -1,15 +1,13 @@
 // Profile config names for nf-core/configs
 
-params {
+profile {
+  cobra {
+    params {
       // Specific nf-core/configs params
       config_profile_contact = 'James Fellows Yates (@jfy133)'
-  config_profile_description = 'nf-core/eager MPCDF profile provided by nf-core/configs'
+      config_profile_description = 'nf-core/eager MPCDF cobra profile provided by nf-core/configs'
-}
+    }
-
+    process {
-profile {
-cobra {
-// Specific nf-core/eager process configuration
-process {
 
       withName: malt {
         maxRetries = 1
@@ -61,4 +59,63 @@ process {
       }
     }
   }
+  raven {
+  // Specific nf-core/eager process configuration
+      params {
+        // Specific nf-core/configs params
+        config_profile_contact = 'James Fellows Yates (@jfy133)'
+        config_profile_description = 'nf-core/eager MPCDF raven profile provided by nf-core/configs'
+      }
+    process {
+
+      withName: malt {
+        maxRetries = 1
+        memory = 2000000.MB
+        cpus = 72
+        time = 24.h
+      }
+      
+      withLabel:'sc_tiny'{
+        cpus = { check_max( 1, 'cpus' ) }
+        memory = { check_max( 1.GB * task.attempt, 'memory' ) }
+        time = 24.h
+      }
+
+      withLabel:'sc_small'{
+        cpus = { check_max( 1, 'cpus' ) }
+        memory = { check_max( 4.GB * task.attempt, 'memory' ) }
+        time = 24.h
+      }
+
+      withLabel:'sc_medium'{
+        cpus = { check_max( 1, 'cpus' ) }
+        memory = { check_max( 8.GB * task.attempt, 'memory' ) }
+        time = 24.h
+      }
+
+      withLabel:'mc_small'{
+        cpus = { check_max( 2 * task.attempt, 'cpus' ) }
+        memory = { check_max( 4.GB * task.attempt, 'memory' ) }
+        time = 24.h
+      }
+
+      withLabel:'mc_medium' {
+        cpus = { check_max( 4 * task.attempt, 'cpus' ) }
+        memory = { check_max( 8.GB * task.attempt, 'memory' ) }
+        time = 24.h
+      }
+
+      withLabel:'mc_large'{
+        cpus = { check_max( 8 * task.attempt, 'cpus' ) }
+        memory = { check_max( 16.GB * task.attempt, 'memory' ) }
+        time = 24.h
+      }
+
+      withLabel:'mc_huge'{
+        cpus = { check_max( 72, 'cpus' ) }
+        memory = { check_max( 240.GB * task.attempt, 'memory' ) }
+        time = 24.h
+      }
+    }
+  }
 }

conf/pipeline/rnaseq/mpcdf.config

@@ -0,0 +1,50 @@
+// Profile config names for nf-core/configs
+
+profiles {
+    cobra {
+        params {
+          // Specific nf-core/configs params
+          config_profile_contact = 'James Fellows Yates (@jfy133)'
+          config_profile_description = 'nf-core/rnaseq MPCDF cobra profile provided by nf-core/configs'
+        }
+        process {
+            cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
+            memory = { check_max( 6.GB * task.attempt, 'memory' ) }
+            time   = { check_max( 4.h  * task.attempt, 'time'   ) }
+
+            errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
+            maxRetries    = 1
+            maxErrors     = '-1'
+
+            // Process-specific resource requirements
+            withLabel:process_low {
+                cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
+                memory = { check_max( 12.GB * task.attempt, 'memory'  ) }
+                time   = { check_max( 4.h   * task.attempt, 'time'    ) }
+            }
+            withLabel:process_medium {
+                cpus   = 40
+                memory = { check_max( 36.GB * task.attempt, 'memory'  ) }
+                time   = { check_max( 6.h   * task.attempt, 'time'    ) }
+            }
+            withLabel:process_high {
+                cpus   = 40
+                memory = { check_max( 72.GB * task.attempt, 'memory'  ) }
+                time   = { check_max( 10.h  * task.attempt, 'time'    ) }
+            }
+            withLabel:process_long {
+                time   = 24.h
+            }
+            withLabel:process_high_memory {
+                cpus   = 40
+                memory = { check_max( 200.GB * task.attempt, 'memory' ) }
+            }
+            withLabel:error_ignore {
+                errorStrategy = 'ignore'
+            }
+            withName:CUSTOM_DUMPSOFTWAREVERSIONS {
+                cache = false
+            }
+        }
+    }
+}

docs/mpcdf.md

@@ -12,24 +12,38 @@ All profiles use `singularity` as the corresponding containerEngine. To prevent
 
 >NB: Nextflow will need to submit the jobs via SLURM to the clusters and as such the commands above will have to be executed on one of the head nodes. Check the [MPCDF documentation](https://www.mpcdf.mpg.de/services/computing).
 
-## cobra
+## Global Profiles
 
-To use: `-profile cobra,mpcdf`
+### cobra
+
+To use: `-profile mpcdf,cobra`
 
 Sets the following parameters:
 
 - Maximum parallel running jobs: 8
-- Max. memory: 750.GB
+- Max. memory: 725.GB
-- Max. CPUs: 80
+- Max. CPUs: 40
 - Max. walltime: 24.h
 
-## raven
+### raven
 
-To use: `-profile raven,mpcdf`
+To use: `-profile mpcdf,raven`
 
 Sets the following parameters:
 
 - Maximum parallel running jobs: 8
-- Max. memory: 368.GB
+- Max. memory: 2000000.MB (2.TB)
-- Max. CPUs: 192
+- Max. CPUs: 72
 - Max. walltime: 24.h
+
+## Pipeline Profiles
+
+### nf-core/eager
+
+We offer a pipeline specific profile optimised for [nf-core/eager](https://nf-co.re/eager)
+
+- Maximum parallel running jobs: 30
+
+### nf-core/rnaseq
+
+We offer a pipeline specific profile optimised for [nf-core/rnaseq](https://nf-co.re/rnaseq)

pipeline/eager.config

@@ -9,7 +9,7 @@
  */
 
 profiles {
-  mpcdf { includeConfig "${params.custom_config_base}/conf/pipeline/eager/mpcdf.config" }
   eva { includeConfig "${params.custom_config_base}/conf/pipeline/eager/eva.config" }
   maestro { includeConfig "${params.custom_config_base}/conf/pipeline/eager/maestro.config" }
+  mpcdf { includeConfig "${params.custom_config_base}/conf/pipeline/eager/mpcdf.config" }
 }

pipeline/rnaseq.config

@@ -10,5 +10,6 @@
 
 profiles {
   eddie { includeConfig "${params.custom_config_base}/conf/pipeline/rnaseq/eddie.config" }
+  mpcdf { includeConfig "${params.custom_config_base}/conf/pipeline/rnaseq/mpcdf.config" }
   utd_sysbio { includeConfig "${params.custom_config_base}/conf/pipeline/rnaseq/utd_sysbio.config" }
 }