Awsbatch adjustments (#724)

* Stashing awsbatch testing * A new test data tsv file for dream data * Remove beforeScript, not needed when the AMI was fixed * No efs tmp mapping in runoptions * Merged sarek-data repo * Added a normal-only dream testdata tsv * Add back time restriction, deal with that later * Updated CHANGELOG.md * Updated Sarek-data to latest master
SciLifeLab · Feb 11, 2019 · e98df24 · e98df24
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commit e98df24
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 -   [#719](https://github.com/SciLifeLab/Sarek/pull/719) - `vepCacheVersion` is now defined in `conf/genomes.config` or `conf/igenomes.config`
 -   [#719](https://github.com/SciLifeLab/Sarek/pull/719) - `snpeff` and `vep` containers are now built with conda
 -   [#716](https://github.com/SciLifeLab/Sarek/pull/716) - Update paths to containers and iGenomes
+-   [#724](https://github.com/SciLifeLab/Sarek/pull/724) - Improved AwsBatch configuration
 
 ### `Added`
 -   [#719](https://github.com/SciLifeLab/Sarek/pull/719) - Possibility to use cache wen annotating with `snpEff` and `VEP`

diff --git a/Sarek-data b/Sarek-data
diff --git a/conf/aws-batch.config b/conf/aws-batch.config
@@ -33,6 +33,9 @@ process {
   maxRetries = 4
   cpus = 2
   memory = 8.GB
+  time = { check_max( 18.h * task.attempt, 'time' ) }
+
+  scratch = true
 
   withName:RunBcftoolsStats {
     cpus = 1