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Awsbatch adjustments #724

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Feb 11, 2019
Merged

Awsbatch adjustments #724

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338c62a
Stashing awsbatch testing
alneberg Jan 28, 2019
1bbf9d7
A new test data tsv file for dream data
alneberg Jan 28, 2019
22a92ef
Remove beforeScript, not needed when the AMI was fixed
alneberg Feb 5, 2019
710c048
No efs tmp mapping in runoptions
alneberg Feb 5, 2019
88b07e1
Merged sarek-data repo
alneberg Feb 5, 2019
152ec5c
Added a normal-only dream testdata tsv
alneberg Feb 5, 2019
785eda7
Merged in dev
alneberg Feb 11, 2019
4ebfa43
Add back time restriction, deal with that later
alneberg Feb 11, 2019
2560694
Updated CHANGELOG.md
alneberg Feb 11, 2019
66900af
Updated Sarek-data to latest master
alneberg Feb 11, 2019
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -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`
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2 changes: 1 addition & 1 deletion Sarek-data
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Submodule Sarek-data updated 1 files
+5 −0 testdata/tsv/dream-test-normal-s3.tsv
3 changes: 3 additions & 0 deletions conf/aws-batch.config
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Expand Up @@ -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
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