diff --git a/CHANGELOG.md b/CHANGELOG.md index 7c62089da..bff232d59 100644 --- 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 index dc58944ba..8266b9c72 100644 --- 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 index ee9883454..daad89f87 100644 --- 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 """ }