Merge pull request #630 from maxibor/dev

Improve memory and error handling of qualimap
nf-core · Dec 11, 2020 · 7ead9a0 · 7ead9a0
2 parents b916b6d + 96135fe
commit 7ead9a0
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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
     """
 }