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Commits on Oct 5, 2016

• Merge pull request #51 from NBISweden/hotfix/v0.2.1

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  viklund

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• Cleaned up workdir

  viklund

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  85e9d3f

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• Merge pull request #49 from NBISweden/release/v0.2

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  viklund

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• Bugfix: show version when not running directly from git

  viklund

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• Correct sorting of files

  viklund

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Commits on Oct 4, 2016

• Forgot a '

  viklund

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• Correct version

  viklund

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• Let users run both annotators, if they really want

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  viklund

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• Structured config file

  viklund

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• Added assembly paramter in the config file

  viklund

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• Small bug fix.

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  viklund

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• Updated README and usage instructions

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Commits on Oct 3, 2016

• Merge pull request #47 from NBISweden/feature/cleanup

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  Andreas Kusalananda Kähäri

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• .gitignore update

  viklund

  committed
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• vt is now installed in the module system on uppmax

  viklund

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• Dynamically assign number of CPUs based on how many we got

  viklund

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• User customizable prefix in result filenames

  viklund

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• Minor cleanup of nextflow.config

  viklund

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• CNVnator is not implemented (yet)

  viklund

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• Clearer intersect step handling

  viklund

  committed
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• Reduce the number of parameters to the workflow.

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  viklund

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• Update variable naming scheme within scripts.

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• Fewer result files and better naming

  viklund

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• Consistent order of process directives

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• More explicit cpu-hour handling

  viklund

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• Merge pull request #46 from NBISweden/feature/vcf_files

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  viklund

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Commits on Sep 29, 2016

• Use vcf-files instead of bed files for all downstream analysis.

  viklund

  committed
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Commits on Sep 21, 2016

• Manta update to 1.0.0 and better run-strategy

  viklund

  committed
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• Merge pull request #44 from NBISweden/feature/better_order

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  viklund

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Commits on Sep 19, 2016

• Combine all the intersected files into one output file.

  viklund

  committed
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• Configure worksteps instead of an option for each tool

  viklund

  committed
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• Some more gitignores

  viklund

  committed
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• Removed production of CALLER_masked_{DEL,INS,DUP}.bed files

  viklund

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• Smarter choosing of executor

  viklund

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• Removed test_data directory

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