/wdl

History for wdl/scripts
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

    Update README.md

    vdauwera committed Apr 21, 2017
    10bd78c
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 Mar 6, 2017
  1. @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 Feb 28, 2017
  1. @vdauwera

    GA4GH Tool Execution Challenge Phase 1

    vdauwera committed Feb 27, 2017
    b57db7e
Commits on Jan 22, 2017
  1. @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

    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 15, 2017
  1. @vdauwera

    Added a script that generates subsets of scatter intervals from a mas… 

    …ter list
    vdauwera committed Jan 7, 2017
    b3eb27d
Commits on Jan 13, 2017
  1. @vdauwera

    New directory for supported-but-not-prod WDLs; includes README and a … 

    …generic options file
    vdauwera committed Jan 8, 2017
    8c9daf3
Commits on Oct 12, 2016
  1. @vdauwera

    Merge pull request #61 from mlin/develop 

    Strike extraneous line from SimpleVariantDiscovery.wdl example (typo probably)
    vdauwera committed on GitHub Oct 12, 2016
    b2e3c09
Commits on Oct 5, 2016

  1. add back inputs and options to the archive for 07/20/16

    Vivek Dasari committed Oct 5, 2016
    ef264f9
Commits on Sep 28, 2016
  1. @mlin

    Strike extraneous line from SimpleVariantDiscovery.wdl example (typo … 

    …probably)
    mlin committed on GitHub Sep 28, 2016
    41083c3
Commits on Sep 27, 2016

  1. Generate new public

    Vivek Dasari committed Sep 27, 2016
    dbf6779
Commits on Sep 9, 2016
  1. @knoblett @knoblett

    Add gatkToWdlWrapper, testWDLTasks.py, all auto-generated WDL tasks f… 

    …or GATK 3.6, and a README to explain use.
    knoblett committed with knoblett Sep 8, 2016
    2f69cf4
Commits on Aug 15, 2016
  1. @sooheelee

    Remove `BETA` label as all links are now live 

    Link to Tutorial#8017 is no longer broken as the article is now public.
    sooheelee committed on GitHub Aug 15, 2016
    d8c1245
Commits on Aug 12, 2016
  1. @sooheelee

    Merge pull request #53 from broadinstitute/shlee_upload_new_scripts 

    WDLs for a GATK tutorial
    sooheelee committed on GitHub Aug 12, 2016
    dce6c85
Commits on Aug 10, 2016
  1. @knoblett @knoblett

    Update filepath, add links to tutorial, add JSONs, add README, rename… 

    … Public pipeline doc
    knoblett committed with knoblett Aug 8, 2016
    4385d17
  2. @sooheelee

    Added WDLs for a GATK tutorial and a readme for the GATK folder 

    	Add WDL scripts and JSON examples for GATK Tutorial#8017
	Add two more tutorial WDLs and modify tutorial_8017.wdl
	Add README.md file for gatk folder
    sooheelee committed Aug 4, 2016
    3e9fe23
Commits on Aug 2, 2016
  1. @vdauwera

    Update bucket filepaths in gotc json

    vdauwera committed Aug 2, 2016
    196c458
Commits on Aug 1, 2016
  1. @vdauwera

    Merge pull request #47 from sooheelee/patch-1 

    Add documentation for PESS pipeline
    vdauwera committed on GitHub Aug 1, 2016
    7eb4a7b
  2. @knoblett @knoblett

    Create jointCallingGenotypes, simpleVariantSelection, simpleVariantDi… 

    …scovery, helloHaplotypeCaller
    knoblett committed with knoblett Jul 28, 2016
    9cdc4fa
  3. @sooheelee

    Add documentation for PESS pipeline 

    Mirrors documentation at <https://software.broadinstitute.org/gatk/documentation/article?id=7899>.
    sooheelee committed on GitHub Aug 1, 2016
    44c56ac
Commits on Jul 28, 2016
  1. @vdauwera

    Replace inputs template with working example

    vdauwera committed Jul 28, 2016
    a24f05f
Commits on Jul 21, 2016
  1. @vdauwera

    Update PairedSingleSampleWf wdl+json to 160720

    vdauwera committed Jul 21, 2016
    1c97908
Commits on Jul 19, 2016
  1. @vdauwera

    Update PairedSingleSampleWf and add JSON

    vdauwera committed Jul 14, 2016
    0e2e852
Commits on Jul 5, 2016
  1. @vdauwera

    Add the production WDL for the GOTC single-sample pipeline

    vdauwera committed Apr 22, 2016
    9b1f513