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This repository has been archived by the owner on Jul 21, 2020. It is now read-only.

Dev #30

Merged
merged 44 commits into from
Jan 13, 2020
Merged

Dev #30

merged 44 commits into from
Jan 13, 2020

Commits on Nov 7, 2018

  1. README.md

    bshifaw committed Nov 7, 2018
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Commits on Feb 1, 2019

  1. Update to gatk4.1

    bshifaw committed Feb 1, 2019
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  2. Updated forum links in Readme

    bshifaw committed Feb 1, 2019
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  3. changed ref file VM path to google bucket path

    bshifaw committed Feb 1, 2019
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  4. Merge branch 'master' into dev

    bshifaw committed Feb 1, 2019
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  5. updated import link to git tag url

    bshifaw committed Feb 1, 2019
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Commits on Apr 2, 2019

  1. Merge branch 'master' of github.com:gatk-workflows/gatk4-somatic-snvs… 

    …-indels into dev
    bshifaw committed Apr 2, 2019
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  2. updated to GATK4.1.1.0

    bshifaw committed Apr 2, 2019
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  3. minor edits

    bshifaw committed Apr 2, 2019
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  4. changed import to dev for pon

    bshifaw committed Apr 2, 2019
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Commits on Apr 4, 2019

  1. updated filter bias variable

    bshifaw committed Apr 4, 2019
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  2. updated filter bias variable

    bshifaw committed Apr 4, 2019
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  3. updated output variable names, removed artifact_mode from normal-normal

    bshifaw committed Apr 4, 2019
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  4. changed index to idx

    bshifaw committed Apr 4, 2019
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  5. removed artifact_modes

    bshifaw committed Apr 4, 2019
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Commits on Apr 5, 2019

  1. updated import to next release: 2.4.0

    bshifaw committed Apr 5, 2019
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  2. specified gatk version in readme

    bshifaw committed Apr 5, 2019
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Commits on Apr 25, 2019

  1. Merge branch 'master' of github.com:gatk-workflows/gatk4-somatic-snvs… 

    …-indels into dev
    bshifaw committed Apr 25, 2019
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  2. Added Funcotator note to readme

    bshifaw committed Apr 25, 2019
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  3. Update to gatk4.1.2.0

    bshifaw committed Apr 25, 2019
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  4. updated input variable for mutect2

    bshifaw committed Apr 25, 2019
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  5. correctin to input vairalbe

    bshifaw committed Apr 25, 2019
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  6. correction to output variable

    bshifaw committed Apr 25, 2019
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Commits on Aug 19, 2019

  1. corrected variable name and simplified json

    bshifaw committed Aug 19, 2019
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  2. Merge branch 'master' into dev

    bshifaw committed Aug 19, 2019
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Commits on Sep 23, 2019

  1. Merge branch 'master' of github.com:gatk-workflows/gatk4-somatic-snvs… 

    …-indels into dev
    bshifaw committed Sep 23, 2019
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  2. renamed input json, removed optional variables from json, updated reg… 

    …ular mutect2 wdl with wdl version 1, updated mutect_pon wdl with wdl version 1
    bshifaw committed Sep 23, 2019
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  3. removed nio wdl

    bshifaw committed Sep 23, 2019
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  4. minor update

    bshifaw committed Sep 23, 2019
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  5. Merge branch 'dev' of github.com:gatk-workflows/gatk4-somatic-snvs-in… 

    …dels into dev
    bshifaw committed Sep 23, 2019
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  6. removed comments in json because later version of cromwell throws err… 

    …or, replaced oncotator in json variables with funcotator
    bshifaw committed Sep 23, 2019
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  7. corrections to import url for pon wdl

    bshifaw committed Sep 23, 2019
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Commits on Sep 26, 2019

  1. mutect2 WDL and pon WDL had inconsistent input names

    bshifaw committed Sep 26, 2019
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  2. mutect2 WDL and pon WDL had inconsistent input names

    bshifaw committed Sep 26, 2019
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  3. added standard_runtime to pon

    bshifaw committed Sep 26, 2019
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  4. add runtime structs

    bshifaw committed Sep 26, 2019
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  5. add runtime structs for mergevcf

    bshifaw committed Sep 26, 2019
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Commits on Sep 27, 2019

  1. Update mutect2_pon.wdl 

    minor spacing edit
    bshifaw committed Sep 27, 2019
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Commits on Sep 30, 2019

  1. cleaned up input variables

    bshifaw committed Sep 30, 2019
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  2. Update README.md 

    Replaced firecloud link with terra
    bshifaw committed Sep 30, 2019
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Commits on Oct 11, 2019

  1. updated docker to 4.1.4.0, updated import url to latest release

    bshifaw committed Oct 11, 2019
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  2. Merge branch 'dev' of github.com:gatk-workflows/gatk4-somatic-snvs-in… 

    …dels into dev
    bshifaw committed Oct 11, 2019
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Commits on Jan 2, 2020

  1. updated docker to 4.1.4.1, updated mutect.wdl to 4.1.4.1 gatk release

    bshifaw committed Jan 2, 2020
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Commits on Jan 3, 2020

  1. Merge branch 'master' into dev

    bshifaw committed Jan 3, 2020
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