From 035ab61f616a4aaf5a6472b4d9d35cbf92531e24 Mon Sep 17 00:00:00 2001
From: pierrespc <pierrespc@gmail.com>
Date: Fri, 8 Oct 2021 09:05:46 +0200
Subject: [PATCH] added unlimitedtime profile to maestro; changed cache for bwa
 process

---
 conf/pipeline/eager/maestro.config | 22 ++++++++++++++++------
 docs/pipeline/eager/maestro.md     |  9 ++++++---
 2 files changed, 22 insertions(+), 9 deletions(-)

diff --git a/conf/pipeline/eager/maestro.config b/conf/pipeline/eager/maestro.config
index 3705d8c..4a6a185 100644
--- a/conf/pipeline/eager/maestro.config
+++ b/conf/pipeline/eager/maestro.config
@@ -2,14 +2,14 @@
  * -------------------------------------------------
  *  Nextflow config file for running nf-core eager on whole genome data or mitogenomes 
  * -------------------------------------------------
- * nextflow run nf-core/eager -profile maestro,<qos>,maestro,<genome> (where <qos> is long or normal and <genome> is nuclear or mitocondrial)
+ * nextflow run nf-core/eager -profile maestro,<qos>,maestro,<genome> (where <qos> is long or normal and <genome> is nuclear, mitocondrial or unlimitedtime)
  */
 
 params {
 
    config_profile_name = 'nf-core/eager nuclear/mitocondrial - human profiles'
 
-   config_profile_description = "Simple profiles for human nuclear or mito genomes"
+   config_profile_description = "Simple profiles for assessing computational ressources that fit human nuclear dna, human mitogenomes processing. unlimitedtime is also available "
 
 }
 
@@ -32,15 +32,16 @@ profiles {
             time = { check_max( 12.h * task.attempt, 'time' ) }
          }
          withName:'bwa'{
-            cpus = { check_max( 30 * task.attempt, 'cpus' ) }
+            cpus = { check_max( 40 * task.attempt, 'cpus' ) }
             memory = { check_max( 40.GB * task.attempt, 'memory' ) }
             time = 24.h 
+            cache = 'deep'
          }
          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' ) }
+            cpus = { check_max( 16 * task.attempt, 'cpus' ) }
+            memory = { check_max( 16.GB * task.attempt, 'memory' ) }
+            time = { check_max( 12.h * task.attempt, 'time' ) }
          }
          withName:'damageprofiler'{
             cpus = 1
@@ -103,4 +104,13 @@ profiles {
          }
       }
    }
+   unlimitedtime {
+     process {
+        errorStrategy = 'finish'
+
+        cpus = 5
+        memory = 200.GB
+        time = 8760.h
+
+    }
 }
diff --git a/docs/pipeline/eager/maestro.md b/docs/pipeline/eager/maestro.md
index 45a151e..d272757 100644
--- a/docs/pipeline/eager/maestro.md
+++ b/docs/pipeline/eager/maestro.md
@@ -14,8 +14,7 @@ Example: `nextflow run nf-core/eager -profile maestro,normal,nuclear`
 
 Specific configurations for maestro has been made for eager.
 
-We decided not to provide any Tool parameter here and focus the profile only for ressource management: Maestro profiles runs with default nf-core/eager parameters, but with modifications concerning time (limit to 24h in normal qos so increasing the memnory and CPUs, specially for alignments).
-
+We decided not to provide any tool parameters here, and focus the profile only for resource management: Maestro profiles runs with default nf-core/eager parameters, but with modifications concerning time (limit to 24h in normal qos, so increasing the memory and CPUs, specially for alignments).
 
 ## nuclear
 
@@ -24,6 +23,10 @@ Increases the number of CPUs and the amount of memory for key processes
 
 ##mitochondrial
 
-more limited computational ressources
+More limited computational resources
 
+##unlimitedtime
+
+Every process has one year time limit. To be used only when some processes can not be completed for time reasons when using mitochondrial or nuclear profiles.  
+Expect slow processes when using this profile because only 5 CPUs are available at a time.