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Pool meth#30

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oneillkza wants to merge 80 commits intoNCBI-Hackathons:masterNCBI-Hackathons/Epigenomics_CWL:masterfrom Epigenomics-Screw:pool_methEpigenomics-Screw/Screw:pool_methCopy head branch name to clipboard

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Commits

Commits on Mar 24, 2017

• Added glitter badge

  neksa

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• quay badge

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Commits on Mar 28, 2017

• Delete copy_number_report.md

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• Delete call_copy_number.md

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• Delete generate_GREAT_report.md

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• Delete pool_single_cells.md

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• Delete generate_summary.md

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• Delete generate_methylation_bigwigs.md

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• Delete run_LOLA.md

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• Delete run_deepcpg.md

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• Delete setup_travis.md

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• Delete datadownload_farlik.md

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• Delete datadownload_smallwood.md

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Commits on Apr 7, 2017

• Update docker file with dependencies for bigwig generation

  

  koneill

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Commits on Apr 10, 2017

• Merge pull request #13 from Epigenomics-Screw/generate_methylation_bigwigs

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• Create base docker file for automatic quay build

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• Create README.md

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• Update README.md

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• Update Dockerfile

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• Removed obsolete Dockerfiles, added base and screw Dockerfiles

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Commits on Apr 11, 2017

• Update README.md

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• Update Dockerfile

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• Create README.md

  neksa

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• Merge pull request #15 from Epigenomics-Screw/neksa

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• Fix Quay badge

  oneillkza

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Commits on Apr 12, 2017

• Create minimal travis test yml

  oneillkza

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• Add Travis badge, try to test Travis

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• Switch to new quay.io

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• New quay.io

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• New quay.io

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• New quay.io

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• New quay.io

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• Try to get methpipe properly installed

  oneillkza

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• Merge pull request #17 from Epigenomics-Screw/master

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• Update Dockerfile

  oneillkza

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Commits on Apr 13, 2017

• Add zlib-dev installs to Screw dockerfile

  oneillkza

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• Update Dockerfile

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• Merge pull request #18 from Epigenomics-Screw/travis_te

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  oneillkza

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Commits on Apr 24, 2017

• clarify CWL nomenclature & add a link

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• Merge pull request #19 from mr-c/patch-1

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Commits on Jun 21, 2017

• Added generation of methylation bigWIGS to preprocess workflow

  

  Chelsey

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Commits on Jun 22, 2017

• Merge pull request #1 from cjfang/pool_meth

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Commits on Jun 27, 2017

• Load libraries first

  

  Chelsey

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• Remove test edits

  

  Chelsey

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• Merge pull request #21 from cjfang/master

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Commits on Jul 5, 2017

• Added poolCpGs.R

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• Pooling DNA methylation calls to create bulk profile

  cjfang

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• Merge pull request #22 from cjfang/master

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Commits on Jul 19, 2017

• Updated working version, added subsetByBed and added typeCheck for Farlik data

  

  Chelsey

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• Merge branch 'master' of https://github.com/cjfang/Screw

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  Chelsey

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• resolve poolCpGs conflict

  

  Chelsey

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• heatmap, pooling, updates to preprocess

  

  Chelsey

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• resolve conflictr

  

  Chelsey

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• resolve other conflict

  

  Chelsey

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• Merge branch 'pool_meth' into pool_meth

  cjfang

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• Merge pull request #23 from cjfang/pool_meth

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Commits on Jul 20, 2017

• Merge pull request #24 from cjfang/master

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• Small edits to subset code

  

  Chelsey

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• Missing bracket

  

  Chelsey

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Commits on Jul 22, 2017

• polish up interconverter, add default value, rename input parameter, fix travis to work with format specification

  

  koneill

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• tweak travis to use correct Docker branch

  

  koneill

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• remove debug detritus

  

  koneill

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• Merge pull request #25 from Epigenomics-Screw/pool_meth

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  oneillkza

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Commits on Jul 24, 2017

• Update README.md

  oneillkza

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Commits on Jul 25, 2017

• Tweak Travis build

  oneillkza

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• change to new quay.io repo

  

  koneill

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• Fix quay.io link

  oneillkza

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Commits on Oct 19, 2017

• Update CODE_OF_CONDUCT.md

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• Update CODE_OF_CONDUCT.md

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• Update CODE_OF_CONDUCT.md

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Commits on Oct 20, 2017

• move cwl up a directory

  

  koneill

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• fix travis to work with new dir structure

  

  koneill

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• Merge branch 'master' into pool_meth

  oneillkza

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• Update .travis.yml

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• Merge pull request #39 from Epigenomics-Screw/pool_meth

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Commits on Oct 21, 2017

• Added converter for additional data sets

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  jjonphl

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• Merge pull request #40 from jjonphl/fix_33

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  oneillkza

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• Fixes pairwise-distance.sh for read-only $indir

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  jjonphl

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• Merge pull request #41 from jjonphl/fix_35

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Commits on Oct 22, 2017

• add example DMR data

  

  koneill

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