Merge pull request nf-core#630 from maxibor/dev

jfy133 · web-flow · commit 7ead9a0d53b9 · 2020-12-11T10:24:02.000+01:00
Improve memory and error handling of qualimap
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 - Removed leftover old DockerHub push CI commands.
 - [#627](https://github.com/nf-core/eager/issues/627) Added de Barros Damgaard citation to README
+- [#630](https://github.com/nf-core/eager/pull/630) Better handling of Qualimap memory requirements and error strategy.
 
 ### `Dependencies`
 
diff --git a/conf/base.config b/conf/base.config
@@ -74,7 +74,7 @@ process {
   }
 
   withName:qualimap{
-    errorStrategy = 'ignore'
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139] ? 'retry' : 'finish' }
   }
 
   withName:preseq {
diff --git a/main.nf b/main.nf
@@ -2443,7 +2443,7 @@ process qualimap {
     script:
     def snpcap = params.snpcapture_bed != '' ? "-gff ${params.snpcapture_bed}" : ''
     """
-    qualimap bamqc -bam $bam -nt ${task.cpus} -outdir . -outformat "HTML" ${snpcap}
+    qualimap bamqc -bam $bam -nt ${task.cpus} -outdir . -outformat "HTML" ${snpcap} --java-mem-size=${task.memory.toGiga()}G
     """
 }
 

Original file line number	Diff line number	Diff line change
`@@ -74,7 +74,7 @@ process {`
`74`	`74`	`}`
`75`	`75`
`76`	`76`	`withName:qualimap{`
`77`		`- errorStrategy = 'ignore'`
	`77`	`+ errorStrategy = { task.exitStatus in [1,143,137,104,134,139] ? 'retry' : 'finish' }`
`78`	`78`	`}`
`79`	`79`
`80`	`80`	`withName:preseq {`
Original file line number	Diff line number	Diff line change
`@@ -2443,7 +2443,7 @@ process qualimap {`
`2443`	`2443`	`script:`
`2444`	`2444`	`def snpcap = params.snpcapture_bed != '' ? "-gff ${params.snpcapture_bed}" : ''`
`2445`	`2445`	`"""`
`2446`		`- qualimap bamqc -bam $bam -nt ${task.cpus} -outdir . -outformat "HTML" ${snpcap}`
	`2446`	`+ qualimap bamqc -bam $bam -nt ${task.cpus} -outdir . -outformat "HTML" ${snpcap} --java-mem-size=${task.memory.toGiga()}G`
`2447`	`2447`	`"""`
`2448`	`2448`	`}`
`2449`	`2449`