Merge pull request #167 from ggabernet/dev

markdup_java_options docs

CHANGELOG.md

@@ -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
 
 ### Changed
 

docs/usage.md

@@ -6,7 +6,7 @@
   - [Reproducibility](#reproducibility)
 - [Main arguments](#main-arguments)
   - [-profile](#-profile)
-  - [`--reads`](#--reads)
+  - [--input](#--input)
   - [--split_fastq](#--split_fastq)
   - [--trim_fastq](#--trim_fastq)
   - [--clip_r1](#--clip_r1)
@@ -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)
@@ -196,7 +197,7 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
   - A profile with a complete configuration for automated testing
   - Includes links to test data so needs no other parameters
 
-### `--reads`
+### --input
 
 Use this to specify the location of your input FastQ files. For example:
 
@@ -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.