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Fix some Sentieon issues #178

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merged 18 commits into from
Apr 22, 2020
Merged

Fix some Sentieon issues #178

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dfc0be8
save dedup bam and recal table
maxulysse Apr 3, 2020
828717d
enable restart from recalibrate with sentieon
maxulysse Apr 7, 2020
a8fb155
simplify tsvpath handling
maxulysse Apr 7, 2020
f6f7001
Merge remote-tracking branch 'upstream/dev' into Sentieon
maxulysse Apr 8, 2020
0b45238
fix bamSentieonTSV.into issue
maxulysse Apr 8, 2020
c69e81b
refactor sentieon channel names
maxulysse Apr 9, 2020
2e1d9fe
Merge remote-tracking branch 'upstream/dev' into Sentieon
maxulysse Apr 15, 2020
08fa021
rename tsv files for Sentieon
maxulysse Apr 15, 2020
7aa0b85
forgot some conflicts
maxulysse Apr 15, 2020
b6037d8
Merge remote-tracking branch 'upstream/dev' into Sentieon
maxulysse Apr 15, 2020
77410fe
Merge remote-tracking branch 'upstream/dev' into Sentieon
maxulysse Apr 17, 2020
397842f
fix merge issue
maxulysse Apr 17, 2020
72a9dca
use deduped bam for Sentieon tools
maxulysse Apr 17, 2020
a4b47d2
update CHANGELOG
maxulysse Apr 17, 2020
428036b
fix input for Sentieon TNscope
maxulysse Apr 17, 2020
281e252
fix #192
maxulysse Apr 21, 2020
f6eb93d
Merge remote-tracking branch 'upstream/dev' into Sentieon
maxulysse Apr 21, 2020
b17313e
Merge branch 'dev' into Sentieon
maxulysse Apr 22, 2020
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -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...)

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