Merge pull request #176 from apeltzer/damageprofiler-more

apeltzer · web-flow · commit f79bc869f1b0 · 2019-04-10T20:03:11.000+02:00
Add more time for DamageProfiler on large ref genomes
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,12 +14,14 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 * Merged in [nf-core/tools](https://github.com/nf-core/tools) release V1.6 template changes  
 
 ### `Fixed`
+* [#152](https://github.com/nf-core/eager/pull/152) - DamageProfiler errors [won't crash entire pipeline anymore](https://github.com/nf-core/eager/issues/171)
+* [#176](https://github.com/nf-core/eager/pull/176) - Increase runtime for DamageProfiler on [large reference genomes](https://github.com/nf-core/eager/issues/173)
 * [#172](https://github.com/nf-core/eager/pull/152) - DamageProfiler errors [won't crash entire pipeline anymore](https://github.com/nf-core/eager/issues/171)
 * [#174](https://github.com/nf-core/eager/pull/190) - Publish DeDup files [properly](https://github.com/nf-core/eager/issues/183) 
 
 ### `Dependencies`
 
-* Added DeDup v0.12.4 (json support)
+* Added DeDup v0.12.5 (json support)
 * Added mtnucratio v0.5 (json support)
 * Updated Picard 2.18.27 -> 2.19.0
 * Updated GATK 4.1.0.0 -> 4.1.1.1
diff --git a/conf/base.config b/conf/base.config
@@ -23,14 +23,15 @@ process {
     memory = { check_max( 2.GB, 'memory' ) }
     cache = false
   }
-  
   withName:convertBam {
     cpus = { check_max(8 * task.attempt, 'cpus') }
   }
   withName:makeSeqDict {
     memory = { check_max( 16.GB * task.attempt, 'memory' ) }
   }
-
+  withname:makeBWAIndex {
+    time = params.large_ref ? '12.h' : { check_max(8.h * task.attempt, 'time') }
+  }
   withName:bwa {
     memory = { check_max( 16.GB * task.attempt, 'memory' ) }
     cpus = { check_max(8 * task.attempt, 'cpus') }
@@ -63,6 +64,7 @@ process {
 
   withName: damageprofiler {
     errorStrategy = 'ignore'
+    params.large_ref ? "time = { check_max(8.h * task.attempt, 'time') }" : "time = { check_max(2.h * task.attempt, 'time') }"
   }
 
   withName: extract_unmapped_reads {

Original file line number	Diff line number	Diff line change
`@@ -23,14 +23,15 @@ process {`
`23`	`23`	`memory = { check_max( 2.GB, 'memory' ) }`
`24`	`24`	`cache = false`
`25`	`25`	`}`
`26`		`-`
`27`	`26`	`withName:convertBam {`
`28`	`27`	`cpus = { check_max(8 * task.attempt, 'cpus') }`
`29`	`28`	`}`
`30`	`29`	`withName:makeSeqDict {`
`31`	`30`	`memory = { check_max( 16.GB * task.attempt, 'memory' ) }`
`32`	`31`	`}`
`33`		`-`
	`32`	`+ withname:makeBWAIndex {`
	`33`	`+ time = params.large_ref ? '12.h' : { check_max(8.h * task.attempt, 'time') }`
	`34`	`+ }`
`34`	`35`	`withName:bwa {`
`35`	`36`	`memory = { check_max( 16.GB * task.attempt, 'memory' ) }`
`36`	`37`	`cpus = { check_max(8 * task.attempt, 'cpus') }`
`@@ -63,6 +64,7 @@ process {`
`63`	`64`
`64`	`65`	`withName: damageprofiler {`
`65`	`66`	`errorStrategy = 'ignore'`
	`67`	`+ params.large_ref ? "time = { check_max(8.h * task.attempt, 'time') }" : "time = { check_max(2.h * task.attempt, 'time') }"`
`66`	`68`	`}`
`67`	`69`
`68`	`70`	`withName: extract_unmapped_reads {`