From 9ea3e2096af742f2449447954b9ca9d75295046f Mon Sep 17 00:00:00 2001
From: pierrespc <pierrespc@gmail.com>
Date: Wed, 29 Sep 2021 13:11:14 +0200
Subject: [PATCH] long and normal qos profiles defined now in an unique maestro
 config file. maestro.config also defined in pipeline/eager for ressources
 assignation to specific processes

---
 conf/maestro.config                | 47 +++++++++++++++++------
 conf/pipeline/eager/maestro.config | 60 ++++++++++++++++++++++++++++++
 pipeline/eager.config              |  1 +
 3 files changed, 96 insertions(+), 12 deletions(-)
 create mode 100644 conf/pipeline/eager/maestro.config

diff --git a/conf/maestro.config b/conf/maestro.config
index a3fb7b5..bf48c23 100644
--- a/conf/maestro.config
+++ b/conf/maestro.config
@@ -10,17 +10,40 @@ singularity {
   runOptions = '--home $HOME:/home/$USER --bind /pasteur'
 }
 
-process {
-  executor = 'slurm'
-  scratch = false
-  queue = 'common'
-  clusterOptions = '--qos=normal'
-}
+profiles {
+    
+    normal {
+        process {
+              executor = 'slurm'
+              scratch = false
+              queue = 'common'
+              clusterOptions = '--qos=normal'
+        }
+
+        params {
+            igenomes_ignore = true
+            igenomesIgnore = true
+            max_memory = 400.GB
+            max_cpus = 96
+            max_time = 24.h
+        }
+    }
+
+    long {
+        process {
+              executor = 'slurm'
+              scratch = false
+              queue = 'common'
+              clusterOptions = '--qos=long'
+        }
+
+        params {
+            igenomes_ignore = true
+            igenomesIgnore = true
+            max_memory = 400.GB
+            max_cpus = 5
+            max_time = 8760.h
+        }
+    }
 
-params {
-  igenomes_ignore = true
-  igenomesIgnore = true
-  max_memory = 400.GB
-  max_cpus = 96
-  max_time = 24.h
 }
diff --git a/conf/pipeline/eager/maestro.config b/conf/pipeline/eager/maestro.config
new file mode 100644
index 0000000..8046c80
--- /dev/null
+++ b/conf/pipeline/eager/maestro.config
@@ -0,0 +1,60 @@
+/*
+ * -------------------------------------------------
+ *  Nextflow config file for running tests
+ * -------------------------------------------------
+ * Defines bundled input files and everything required
+ * to run a fast and simple test. Use as follows:
+ * nextflow run nf-core/eager -profile test, docker (or singularity, or conda)
+ */
+
+params {
+
+   config_profile_name = 'nf-core/eager nucleaer - human profile'
+
+   config_profile_description = "A simple profile for human nuclear genomes"
+
+   email = 'pluisi@pasteur.fr'
+}
+
+
+process {
+   errorStrategy = 'retry'
+   maxRetries = 2
+
+   withName:'makeBWAIndex'{
+      cpus = { check_max( 8 * task.attempt, 'cpus' ) }
+      memory = { check_max( 8.GB * task.attempt, 'memory' ) }
+      time = { check_max( 12.h * task.attempt, 'time' ) }
+   }
+   withName:'adapter_removal'{
+      cpus = { check_max( 8 * task.attempt, 'cpus' ) }
+      memory = { check_max( 16.GB * task.attempt, 'memory' ) }
+      time = { check_max( 12.h * task.attempt, 'time' ) }
+   }
+   withName:'bwa'{
+      cpus = { check_max( 15 * task.attempt, 'cpus' ) }
+      memory = { check_max( 16.GB * task.attempt, 'memory' ) }
+      time = 24.h 
+   }
+   withName:'markduplicates'{
+      errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
+      cpus = { check_max( 8 * task.attempt, 'cpus' ) }
+      memory = { check_max( 8.GB * task.attempt, 'memory' ) }
+      time = { check_max( 6.h * task.attempt, 'time' ) }
+   }
+   withName:'damageprofiler'{
+      cpus = 1
+      memory = { check_max( 8.GB * task.attempt, 'memory' ) }
+      time = { check_max( 6.h * task.attempt, 'time' ) }
+   }
+   withName:'fastp'{
+      cpus = 8 
+      memory = { check_max( 8.GB * task.attempt, 'memory' ) }
+      time = { check_max( 6.h * task.attempt, 'time' ) }
+   }
+   withName:'fastqc'{
+      cpus = 2
+      memory = { check_max( 8.GB * task.attempt, 'memory' ) }
+      time = { check_max( 6.h * task.attempt, 'time' ) }
+   }
+}
diff --git a/pipeline/eager.config b/pipeline/eager.config
index 3e47276..352395b 100644
--- a/pipeline/eager.config
+++ b/pipeline/eager.config
@@ -11,4 +11,5 @@
 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/maestro.config" }
 }