From f6266879d6a94ee3f442cae6a4efaa7c2e85f1ab Mon Sep 17 00:00:00 2001
From: pierrespc <pierrespc@gmail.com>
Date: Wed, 29 Sep 2021 13:47:35 +0200
Subject: [PATCH] edited maestronuclear and maestromitocondrial configs. The
 latter has not been optimized yet

---
 .../pipeline/eager/maestromitocondrial.config | 58 +++++++++++++++++++
 conf/pipeline/eager/maestronuclear.config     |  6 +-
 pipeline/eager.config                         |  1 +
 3 files changed, 61 insertions(+), 4 deletions(-)
 create mode 100644 conf/pipeline/eager/maestromitocondrial.config

diff --git a/conf/pipeline/eager/maestromitocondrial.config b/conf/pipeline/eager/maestromitocondrial.config
new file mode 100644
index 0000000..62c6e4e
--- /dev/null
+++ b/conf/pipeline/eager/maestromitocondrial.config
@@ -0,0 +1,58 @@
+/*
+ * -------------------------------------------------
+ *  Nextflow config file for running nf-core eager on mitocondrial data (providing reference genome only the reference genome for mitogenomes)_
+ * -------------------------------------------------
+ * nextflow run nf-core/eager -profile maestro,<qos>,maestromitocondrial (where <qos> is long or normal)
+ */
+
+params {
+
+   config_profile_name = 'nf-core/eager mitrocondrial - human profile'
+
+   config_profile_description = "A simple profile for human mitogenomes"
+
+   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( 5 * task.attempt, 'cpus' ) }
+      memory = { check_max( 5.GB * task.attempt, 'memory' ) }
+      time = 24.h 
+   }
+   withName:'markduplicates'{
+      errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
+      cpus = { check_max( 5 * task.attempt, 'cpus' ) }
+      memory = { check_max( 5.GB * task.attempt, 'memory' ) }
+      time = { check_max( 6.h * task.attempt, 'time' ) }
+   }
+   withName:'damageprofiler'{
+      cpus = 1
+      memory = { check_max( 5.GB * task.attempt, 'memory' ) }
+      time = { check_max( 3.h * task.attempt, 'time' ) }
+   }
+   withName:'fastp'{
+      cpus = 8 
+      memory = { check_max( 5.GB * task.attempt, 'memory' ) }
+      time = { check_max( 3.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/conf/pipeline/eager/maestronuclear.config b/conf/pipeline/eager/maestronuclear.config
index 8046c80..7ec6a9c 100644
--- a/conf/pipeline/eager/maestronuclear.config
+++ b/conf/pipeline/eager/maestronuclear.config
@@ -1,10 +1,8 @@
 /*
  * -------------------------------------------------
- *  Nextflow config file for running tests
+ *  Nextflow config file for running nf-core eager on whole genome data 
  * -------------------------------------------------
- * 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)
+ * nextflow run nf-core/eager -profile maestro,<qos>,maestronuclear (where <qos> is long or normal)
  */
 
 params {
diff --git a/pipeline/eager.config b/pipeline/eager.config
index 9758f0d..5825bab 100644
--- a/pipeline/eager.config
+++ b/pipeline/eager.config
@@ -12,4 +12,5 @@ profiles {
   mpcdf { includeConfig "${params.custom_config_base}/conf/pipeline/eager/mpcdf.config" }
   eva { includeConfig "${params.custom_config_base}/conf/pipeline/eager/eva.config" }
   maestronuclear { includeConfig "${params.custom_config_base}/conf/pipeline/eager/maestronuclear.config" }
+  maestromitocondrial { includeConfig "${params.custom_config_base}/conf/pipeline/eager/maestromitocondrial.config" }
 }