pre-template-update

This release is the most recent prior to the repository changes needed to migrate builds from Travis to Gitlab.

What's Changed

• fix: decodeuri by @Shenglai in #104
• BINF-520: add wf to support ar submission by @Shenglai in #108
• [BINF-608] updated gatk and picard images by @tzuni in #109
• Fix/log4j patch by @tzuni in #110
• Fix/picard to sql calling by @tzuni in #111
• Fix/load bai key by @tzuni in #113
• Feat/update readme by @tzuni in #114
• BINF-655: fix bai upload for ar workflow by @Shenglai in #115
• BINF-640: change base image by @Shenglai in #116

New Contributors

• @tzuni made their first contribution in #109

Full Changelog: 2.0...pre-template-update

v2.0

Feat/BINF-309: DNA-Seq revamp (#103)

* feat(BINF-309): removing old
* feat(BINF-309): streamline bamfastq
* feat(clean): tmp mv
* feat(extract): standardize
* feat(BINF-309): standarize extract
* feat(bwa): std bwa wfs
* feat(BINF-309): rg matching tests
* feat(metrics): add metrics wfs
* feat(decider): markdup
* feat(format): format tools
* feat(picard): sqlite
* fix(format): validation fixes
* feat(picard): reduce validation
* feat(integrity): remove wf
* chore(docs): starting rewrite of docs
* feat(inputs): rm header file
* chore(rename): rename and organize
* chore(organize): group wfs
* chore(doc): update main wf name
* fix(tests): update wf paths
* feat(expr): add function to expression_lib for fastq_cleaner
* BINF-372: add example input json for external users
* chore(doc): update readme
Co-authored-by: Kyle Hernandez <khernandez@bsd.uchicago.edu>
Co-authored-by: Shenglai <sli6@uchicago.edu>

v1.2

Merge pull request #102 from NCI-GDC/feat/detect-secrets

(feat) initialize detect-secrets

1.1: Merge pull request #49 from NCI-GDC/featdev/ga4gh

Featdev/ga4gh

1.0: Merge pull request #48 from NCI-GDC/featdev/ga4gh

add ftp_proxy to curl and fix the uuid

20161118

Update README.md