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markdup_java_options docs #167

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Mar 30, 2020
Merged

markdup_java_options docs #167

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markdup_java_options docs
ggabernet Mar 27, 2020
674e156
update to params input in docs
ggabernet Mar 29, 2020
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maxulysse Mar 30, 2020
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -17,6 +17,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
- [#158](https://github.com/nf-core/sarek/pull/158) - Added `ggplot2` version `3.3.0`
- [#163](https://github.com/nf-core/sarek/pull/163) - Add [MSIsensor](https://github.com/ding-lab/msisensor) in tools and container
- [#164](https://github.com/nf-core/sarek/pull/164) - Add `--no_gatk_spark` params and tests
- [#166](https://github.com/nf-core/sarek/issues/166) - Add `--markdup_java_options` documentation

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9 changes: 9 additions & 0 deletions docs/usage.md
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Expand Up @@ -79,6 +79,7 @@
- [Job resources](#job-resources)
- [Automatic resubmission](#automatic-resubmission)
- [Custom resource requests](#custom-resource-requests)
- [--markdup_java_options](#--markdup_java_options)
- [AWSBatch specific parameters](#awsbatch-specific-parameters)
- [--awsqueue](#--awsqueue)
- [--awsregion](#--awsregion)
Expand Down Expand Up @@ -777,6 +778,14 @@ You can then create a pull request to the `nf-core/configs` repository with the

If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack).

## --markdup_java_options

To control the java options necessary for the GATK `MarkDuplicates` process, you can set this parameter. For example (those are the default settings):

```bash
--markdup_java_options "-Xms4000m -Xmx7g"
```

## AWSBatch specific parameters

Running the pipeline on AWSBatch requires a couple of specific parameters to be set according to your AWSBatch configuration.
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