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Commits on Nov 11, 2019

• Update README.md

  tjbencomo

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Commits on Apr 25, 2019

• Update example files and reformat reference template

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• Add variant_calling references to the references template file. This closes #6

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• Merge branch 'master' of https://github.com/tjbencomo/variant-discovery-pipeline

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• Close #8

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Commits on Apr 23, 2019

• Update README.md

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• Update README.md

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• Clean up variant_calling.wdl so it should be up and functional

  tjbencomo

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• Add functionality to auto generate input file for variant calling pipe

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Commits on Apr 18, 2019

• Add template file for references and example input files

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• Update README.md

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• Update README.md

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Commits on Apr 17, 2019

• Update preprocessing section

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Commits on Apr 16, 2019

• Job submission up and running

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• Remove PU from preprocessing for now as unsure how PU should be specified

  tjbencomo

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• preprocess.py seems to be working up to at least submitting the jobs

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Commits on Apr 15, 2019

• Initial code finished. Now need to test and clear up FASTQ read group details with Michael

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Commits on Apr 14, 2019

• Add WDL wrapper for preprocessing workflow

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Commits on Apr 8, 2019

• Add .gitignore

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• Initial commit variant_calling.wdl. Still need to test

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• Add CopyOutputs task. Delete native output instructions in workflow

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Commits on Apr 2, 2019

• Merge branch 'master' of https://github.com/tjbencomo/variant-discovery-pipeline

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• Minor changes

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• Working preprocessing.wdl and add temporary-directory variable to config file so JVM tmp dir is set to use /tmp/cromwell, not the cromwell root executions folder. This was causing major slowdown du…

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Commits on Mar 29, 2019

• Update README.md

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• Update README.md

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• Add QC report info

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• Update README.md

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Commits on Feb 18, 2019

• Update README.md

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Commits on Jan 9, 2019

• Merge branch 'master' of https://github.com/tjbencomo/variant-discovery-pipeline

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• Add column counting number of SCCs with nonsynonymous_SNV, stopgain, and splicing mutations. Add complementary column containing names of samples that have these kinds of mutations

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Commits on Dec 26, 2018

• Update README.md

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• Update README.md

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• Remove unused imports and update documentation

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• Refactor function names. Remove save_summary() method - now directly use to_csv() pandas call.

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