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Markdup java options #774

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Mar 26, 2019
Merged

Markdup java options #774

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fa2e2d3
auto generates memory for MD when less than 8G is available
maxulysse Mar 25, 2019
7cfedd0
add CHANGELOG
maxulysse Mar 25, 2019
7b1233b
trying to fix TravisCI
maxulysse Mar 26, 2019
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.

- [#753](https://github.com/SciLifeLab/Sarek/pull/753) - Update `binac`, `cfc` configuration
- [#766](https://github.com/SciLifeLab/Sarek/pull/766) - Added `ps` in `r-base` and `runallelecount` containers
- [#XXX](https://github.com/SciLifeLab/Sarek/pull/XXX) - Autogenerates memory requirements from MarkDuplicates when less that 8G is available. cf [nf-core/rnaseq#179](https://github.com/nf-core/rnaseq/pull/179)

### `Fixed`

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3 changes: 2 additions & 1 deletion main.nf
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Expand Up @@ -302,8 +302,9 @@ process MarkDuplicates {
when: step == 'mapping' && !params.onlyQC

script:
markdup_java_options = (task.memory.toGiga() > 8) ? ${params.markdup_java_options} : "\"-Xms" + (task.memory.toGiga() / 2 )+"g "+ "-Xmx" + (task.memory.toGiga() - 1)+ "g\""
"""
gatk --java-options ${params.markdup_java_options} \
gatk --java-options ${markdup_java_options} \
MarkDuplicates \
--MAX_RECORDS_IN_RAM 50000 \
--INPUT ${idSample}.bam \
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