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Release 6.0.0 #426

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merged 7 commits into from
Sep 24, 2020
Merged

Release 6.0.0 #426

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7c27779
changelog for 6.0.0
hassanfa Sep 22, 2020
5be5903
Development model changed to gitflow
hassanfa Sep 22, 2020
dd6860d
Development model changed to gitflow
hassanfa Sep 22, 2020
c3170b7
Development model changed to gitflow
hassanfa Sep 22, 2020
5de918b
changelog updated
hassanfa Sep 22, 2020
e1679b2
Add numpy as dependency
hassanfa Sep 23, 2020
d2ac8cf
Add numpy as dependency
hassanfa Sep 23, 2020
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27 changes: 24 additions & 3 deletions CHANGELOG.rst
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@@ -1,17 +1,38 @@

[6.0.0]
-------

Added
^^^^^
* UMI workflow using Sentieon tools. Analysis run available via `balsamic run analysis --help` command. PR #359
* VCFutils to create VCF from flat text file. This is for internal purpose to generate validation VCF. PR #349
* Download option for hg38 (not validated) PR #407
* Option to disable variant callers for WES runs. PR #417

Fixed
^^^^^
* Missing cyvcf2 dependency, and changed conda environment for base environment PR #413
* Missing numpy dependency PR #426

Changed
^^^^^^^
* COSMIC db for hg19 updated to v90 PR #407
* Fastp trimming is now a two-pass trimming and adapter trimming is always enabled. This might affect coverage slightly PR #422
* All containers start with a clean environment #425
* All Sentieon environment variables are now added to config when workflow executes #425
* Branching model will be changed to gitflow

[5.1.0]
-------

Fixed
^^^^^
* Vardict-java version fixed. This is due to bad dependency and releases available on conda. Anaconda is not yet update
with vardict 1.8, but vardict-java 1.8 is there. This causes various random breaks with Vardict's TSV output. #403
* Vardict-java version fixed. This is due to bad dependency and releases available on conda. Anaconda is not yet update with vardict 1.8, but vardict-java 1.8 is there. This causes various random breaks with Vardict's TSV output. #403

Changed
^^^^^^^
* Refactored Docker files a bit, preparation for decoupling #403


Removed
^^^^^^^
* In preparation for GATK4, IndelRealigner is removed #404
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2 changes: 1 addition & 1 deletion README.rst
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Expand Up @@ -30,7 +30,7 @@ Snakemake cli given that there is a proper config file created.
* - Author
- Hassan Foroughi Asl
* - Development model
- Github Flow, release branch
- Gitflow
* - Build status
- |travis_status_badge|_
* - Container latest release status
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3 changes: 2 additions & 1 deletion requirements.txt
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Expand Up @@ -12,4 +12,5 @@ jinja2
networkx
colorclass
pydantic
cyvcf2<0.10.0
numpy
cyvcf2<0.10.0