Merge pull request #518 from nf-core/bedtools-fix

Bedtools fix

Author: jfy133

CHANGELOG.md

@@ -45,6 +45,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 * [#497](https://github.com/nf-core/eager/issues/497) - Simplifies number of parameters required to run bam filtering
 * [#501](https://github.com/nf-core/eager/issues/501) - Adds additional validation checks for MALT/MaltExtract database input files
 * [#508](https://github.com/nf-core/eager/issues/508) - Made Markduplicates default dedupper due to narrower context specificity of dedup
+* [#516](https://github.com/nf-core/eager/issues/516) - Made bedtools not report out of memory exit code when warning of inconsistant FASTA/Bed entry names
 
 ### `Dependencies`
 

main.nf

@@ -2026,8 +2026,8 @@ process bedtools {
 
   script:
   """
-  bedtools coverage -a ${anno_file} -b $bam | pigz -p ${task.cpus} > "${bam.baseName}".breadth.gz
-  bedtools coverage -a ${anno_file} -b $bam -mean | pigz -p ${task.cpus} > "${bam.baseName}".depth.gz
+  bedtools coverage -nonamecheck -a ${anno_file} -b $bam | pigz -p ${task.cpus} > "${bam.baseName}".breadth.gz
+  bedtools coverage -nonamecheck -a ${anno_file} -b $bam -mean | pigz -p ${task.cpus} > "${bam.baseName}".depth.gz
   """
 }