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Commits on Jun 28, 2017
  1. @vdauwera

    Take over Google's wdl_runner

    vdauwera committed Jun 28, 2017
    4c400a2
Commits on Jun 7, 2017
  1. @ruchim

    pair syntax (#114)

    ruchim committed on GitHub Jun 7, 2017
    d336f91
Commits on May 24, 2017
  1. @cjllanwarne

    Merge pull request #113 from broadinstitute/cjl_basename_docs 

    Docs for basename
    cjllanwarne committed on GitHub May 24, 2017
    09bf31e
  2. @cjllanwarne

    Docs for basename

    cjllanwarne committed May 24, 2017
    885888a
Commits on May 9, 2017
  1. @geoffjentry

    Move grammar.hgr and add makefiles (#111)

    geoffjentry committed on GitHub May 9, 2017
    048dc55
Commits on Apr 28, 2017
  1. @sooheelee

    Remove pipe image URLs that do not display 

    So as not to confuse readers
    sooheelee committed on GitHub Apr 28, 2017
    6e67179
  2. @sooheelee

    Fix image links that broke during archiving 

    Use image URLs from <http://gatkforums.broadinstitute.org/gatk/discussion/7899>.
    sooheelee committed on GitHub Apr 28, 2017
    2041847
Commits on Apr 21, 2017
  1. @vdauwera

    Merge pull request #105 from broadinstitute/vdauwera-readme_tweaks 

    Trivial updates to note limitations of the scripts we provide.
    vdauwera committed on GitHub Apr 21, 2017
    393fcb8
  2. @vdauwera

    Update README.md

    vdauwera committed Apr 21, 2017
    10bd78c
Commits on Apr 19, 2017
  1. @vdauwera

    Merge pull request #103 from broadinstitute/gvda_update_gotc_wdl 

    Update supported GOTC single-sample and add pipeline documentation
    vdauwera committed on GitHub Apr 19, 2017
    bf45763
Commits on Apr 11, 2017
  1. @vdauwera

    Update supported GOTC single-sample and add pipeline documentation

    vdauwera committed Apr 11, 2017
    2d6595e
  2. @vdauwera

    Update GOTC single-sample workflow to functional equivalence version

    vdauwera committed Apr 11, 2017
    a887782
Commits on Apr 10, 2017
  1. @cjllanwarne

    Merge pull request #98 from broadinstitute/cjl_C25_update 

    Optionals methods and pair literals
    cjllanwarne committed on GitHub Apr 10, 2017
    c84ade7
  2. @cjllanwarne

    Optionals methods and pair literals

    cjllanwarne committed Mar 3, 2017
    52e3c0c
Commits on Apr 3, 2017
  1. @cjllanwarne

    Merge pull request #100 from broadinstitute/cjl_if_else_expressions 

    if then else expressions
    cjllanwarne committed on GitHub Apr 3, 2017
    3cdd802
  2. @cjllanwarne

    if then else expressions

    cjllanwarne committed Mar 26, 2017
    61d7a84
  3. @cjllanwarne

    Merge pull request #101 from broadinstitute/js_interloper_pullapprove 

    Adding jsotobroad to pullapprover members list
    cjllanwarne committed on GitHub Apr 3, 2017
    8b34c4c

  4. Adding jsotobroad to pullapprover members list

    jsotobroad committed Apr 3, 2017
    7761379
Commits on Mar 6, 2017
  1. @vdauwera

    Merge pull request #88 from broadinstitute/gvda_standalone_calling_steps 

    Standalone variant calling steps + joint discovery
    vdauwera committed on GitHub Mar 6, 2017
    7e6f95b
  2. @vdauwera

    WDLs for segments of the germline short variant calling pipeline 

        - HaplotypeCaller GVCF scatter-gathered across intervals
    - GenotypeGVCFs scatter-gathered across intervals
    - VQSR (no scatter)
    - Joint discovery (GGVCFs through VQSR, no genotype refinement)
    vdauwera committed Jan 22, 2017
    2c56658
Commits on Mar 4, 2017
  1. @vdauwera

    Merge pull request #97 from broadinstitute/gvda_ga4gh_tools_phase1 

    GA4GH Tool Execution Challenge Phase 1
    vdauwera committed on GitHub Mar 4, 2017
    a8b6234
Commits on Feb 28, 2017
  1. @vdauwera

    GA4GH Tool Execution Challenge Phase 1

    vdauwera committed Feb 27, 2017
    b57db7e
Commits on Feb 24, 2017
  1. @geoffjentry

    checkpoint

    geoffjentry committed Feb 24, 2017
    7bdd8fd
Commits on Feb 22, 2017
  1. @sidoruka @geoffjentry

    JavaScript support for a Hermes WDL grammar (#94) 

    * JavaScript support for a Hermes WDL grammar
    sidoruka committed with geoffjentry Feb 22, 2017
    86f4916
  2. @Horneth @geoffjentry

    update grammar file to match Cromwell supported WDL version (#95)

    Horneth committed with geoffjentry Feb 22, 2017
    90f3514
Commits on Feb 8, 2017
  1. @kshakir

    Added katevoss and alphabetized pullapprove

    kshakir committed Feb 8, 2017
    fa88c3b
Commits on Jan 23, 2017
  1. @mcovarr

    Merge pull request #85 from broadinstitute/mlc_prefix_redux 

    prefix redux
    mcovarr committed on GitHub Jan 23, 2017
    35faef8
  2. @geoffjentry

    add ruchi

    geoffjentry committed on GitHub Jan 23, 2017
    16c6244
  3. @mcovarr

    prefix redux

    mcovarr committed Jan 17, 2017
    1387e51
Commits on Jan 22, 2017
  1. @vdauwera

    Merge pull request #83 from broadinstitute/gvda_reversion_wdls 

    WDLs to revert/convert between BAM, FASTQ and uBAM
    vdauwera committed on GitHub Jan 22, 2017
    7ac575f
  2. @vdauwera

    WDLs for generic conversion/reversion use cases 

     - revert batch of single-readgroup SAM/BAMs to FASTQ
 - convert batch of paired FASTQs to uBAM per readgroup
 - revert multi-readgroup SAM/BAM to uBAM
    vdauwera committed Jan 8, 2017
    575a3c3
Commits on Jan 21, 2017
  1. @vdauwera

    Merge pull request #82 from broadinstitute/gvda_trivial_bam_manipulation 

    WDLs for trivial bam manipulation
    vdauwera committed on GitHub Jan 21, 2017
    9f7bfa8
  2. @vdauwera

    WDLs for trivial BAM manipulations 

        - WDL to extract the SAM headers from a list of BAMs
    - WDL to validate a list of SAM/BAM files
    vdauwera committed Jan 8, 2017
    dc8d09d
Commits on Jan 17, 2017
  1. @mcovarr

    Merge pull request #84 from broadinstitute/mlc_join 

    prefix() proposal.  Closes broadinstitute/cromwell#375
    mcovarr committed on GitHub Jan 17, 2017
    944ebea
  2. @mcovarr

    prefix() proposal. Closes broadinstitute/cromwell#375

    mcovarr committed Jan 9, 2017
    8ec60c2