Merge pull request #178 from MaxUlysse/Sentieon

Fix some Sentieon issues
nf-core · Apr 22, 2020 · c1bdcbf · c1bdcbf
2 parents 73c6a33 + b17313e
commit c1bdcbf
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -80,6 +80,7 @@ Piellorieppe is one of the main massif in the Sarek National Park.
 - [#164](https://github.com/nf-core/sarek/pull/164) - Fix issues when running with `Sentieon`
 - [#164](https://github.com/nf-core/sarek/pull/164) - Add more VCFs to annotation
 - [#167](https://github.com/nf-core/sarek/pull/167) - Add `--markdup_java_options` documentation to fix [#166](https://github.com/nf-core/sarek/issues/166)
+- [#178](https://github.com/nf-core/sarek/pull/178) - Fix `Sentieon` variant calling, now using deduped bam files
 - [#188](https://github.com/nf-core/sarek/pull/188) - Fix input/output channels for process `IndexBamFile` to match actual files in the `mapped.tsv` files
 - [#189](https://github.com/nf-core/sarek/pull/189) - Fix `no_intervals` for process `HaplotypeCaller` (the file just need to actually exists...)