Merge pull request #114 from apeltzer/bwamem

Add sane defaults for BWA mem

Author: apeltzer

CHANGELOG.md

@@ -9,7 +9,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ### `Added`
 * [#111](https://github.com/nf-core/eager/pull/110) - Allow [Zipped FastA reference input](https://github.com/nf-core/eager/issues/91)
 * [#113](https://github.com/nf-core/eager/pull/113) - All files are now staged via channels, which is considered best practice by Nextflow. 
-
+* [#114](https://github.com/nf-core/eager/pull/113) - Add proper runtime defaults for multiple processes 
 
 ### `Fixed`
 * [#110](https://github.com/nf-core/eager/pull/110) - Fix for [MultiQC Missing Second FastQC report](https://github.com/nf-core/eager/issues/107)

conf/base.config

@@ -34,6 +34,20 @@ process {
     cpus = { check_max(8 * task.attempt, 'cpus') }
     time = { check_max(8.h * task.attempt, 'time') }
   }
+  withName:bwamem{
+    memory = { check_max( 16.GB * task.attempt, 'memory' ) }
+    cpus = { check_max(8 * task.attempt, 'cpus') }
+    time = { check_max(8.h * task.attempt, 'time') }
+  }
+  withName:qualimap{
+    cpus = { check_max(8 * task.attempt, 'cpus') }
+  }
+  withName:bam_trim{
+    cpus = { check_max(4 * task.attempt, 'cpus') }
+  }
+  withName:markDup{
+    cpus = { check_max(8 * task.attempt, 'cpus') }
+  }
   withName:preseq {
     errorStrategy = 'ignore'
   }