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Merged
maxulysse merged 3 commits into from
Jul 23, 2020
Merged

update docs and comments #255

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d7b7ed5
update docs and comments
maxulysse Jul 14, 2020
f562c63
Apply suggestions from code review
maxulysse Jul 23, 2020
9813521
Merge branch 'dev' into docs
apeltzer Jul 23, 2020
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -8,11 +8,13 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a

### Added

- [#230](https://github.com/nf-core/sarek/pull/230) - Add `ignore_soft_clipped_bases` option for `Mutect2` [#218](https://github.com/nf-core/sarek/issues/218)
- [#145](https://github.com/nf-core/sarek/pull/145) - Add `UMI annotation and consensus` functionality to Sarek

### Changed

- [#237](https://github.com/nf-core/sarek/pull/237) - Switch `bwa 0.7.17` for `bwa-mem2 2.0`
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- [#255](https://github.com/nf-core/sarek/pull/255) - Update docs

### Fixed

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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -104,6 +104,7 @@ Helpful contributors:
* [Marcel Martin](https://github.com/marcelm)
* [Nilesh Tawari](https://github.com/nilesh-tawari)
* [Olga Botvinnik](https://github.com/olgabot)
* [Paul Cantalupo](https://github.com/pcantalupo)
* [Phil Ewels](https://github.com/ewels)
* [Sabrina Krakau](https://github.com/skrakau)
* [Sebastian-D](https://github.com/Sebastian-D)
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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -66,7 +66,7 @@ params {
no_strelka_bp = null // Strelka will use Manta candidateSmallIndels if available
pon = false // No default PON (Panel of Normals) file for GATK Mutect2 / Sentieon TNscope
pon_index = false // No default PON index for GATK Mutect2 / Sentieon TNscope
ignore_soft_clipped_bases = null // GATK Mutect2
ignore_soft_clipped_bases = null // enable --dont-use-soft-clipped-bases for GATK Mutect2
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// Annotation
annotate_tools = null // Only with --step annotate
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