broadinstitute/wdl

Commits on Oct 6, 2016

Add remaining GATK 3.6 tool workflows.

knoblett committed on GitHub Oct 6, 2016

55d9318
Move to GATKToolWorkflows_3.6 subfolder

knoblett committed on GitHub Oct 6, 2016

dc1be28
Upload AnalyzeCovariates wdl script

knoblett committed on GitHub Oct 6, 2016

9965d74
Rename to remove "Firecloud" in file name

knoblett committed on GitHub Oct 6, 2016

ec54088

Commits on Oct 4, 2016

Create gatkToWdlWrapper_Firecloud.py

knoblett committed on GitHub Oct 4, 2016

230de7c

Commits on Sep 9, 2016

Merge pull request #58 from broadinstitute/knoblett-gatkWrapper
```
Add gatkToWdlWrapper
```
knoblett committed on GitHub Sep 9, 2016
b35001a
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

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

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

Merge pull request #52 from broadinstitute/knoblett-updatePaths
```
Update filepath, add links to tutorial, add JSONs, add README, rename Public pipeline doc
```
knoblett committed on GitHub Aug 10, 2016
124a2cc
Update filepath, add links to tutorial, add JSONs, add README, rename…
```
… Public pipeline doc
```
knoblett committed with knoblett Aug 8, 2016
4385d17

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

Merge pull request #48 from broadinstitute/gvda_update_gotc_json_buck…
```
…etpaths

Update bucket filepaths in gotc json
```
vdauwera committed on GitHub Aug 2, 2016
57f9165
Update bucket filepaths in gotc json

vdauwera committed Aug 2, 2016

196c458

Commits on Aug 1, 2016

Merge pull request #47 from sooheelee/patch-1
```
Add documentation for PESS pipeline
```
vdauwera committed on GitHub Aug 1, 2016
7eb4a7b
Merge pull request #46 from broadinstitute/knoblett-forumWdls
```
Add WDL scripts from forum
```
knoblett committed on GitHub Aug 1, 2016
0fd3809
Create jointCallingGenotypes, simpleVariantSelection, simpleVariantDi…
```
…scovery, helloHaplotypeCaller
```
knoblett committed with knoblett Jul 28, 2016
9cdc4fa
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

Merge pull request #45 from broadinstitute/gvda_update_inputs_json
```
Replace inputs template with working example
```
vdauwera committed on GitHub Jul 28, 2016
b26ee3f
Replace inputs template with working example

vdauwera committed Jul 28, 2016

a24f05f

Commits on Jul 21, 2016

Merge pull request #44 from broadinstitute/gvda_update_singsampwdl_16…
```
…0720

Update PairedSingleSampleWf wdl+json to 160720
```
vdauwera committed on GitHub Jul 21, 2016
cc053ad
Update PairedSingleSampleWf wdl+json to 160720

vdauwera committed Jul 21, 2016

1c97908

Commits on Jul 19, 2016

Merge pull request #42 from broadinstitute/gvda_update_public_broad_p…
```
…rod_wdls

Update PairedSingleSampleWf and add JSON of inputs
```
vdauwera committed on GitHub Jul 19, 2016
7fae872
Update PairedSingleSampleWf and add JSON

vdauwera committed Jul 14, 2016

0e2e852

Commits on Jul 7, 2016

Merge pull request #41 from broadinstitute/gvda_fixlink
```
Fixed broken link
```
kcibul committed on GitHub Jul 7, 2016
f1c8e37
Merge pull request #36 from broadinstitute/gvda_add_scripts_section
```
Add the production WDL for the GOTC single-sample pipeline + READMEs
```
vdauwera committed on GitHub Jul 7, 2016
ee6c0da

Commits on Jul 5, 2016

Add the production WDL for the GOTC single-sample pipeline

vdauwera committed Apr 22, 2016

9b1f513

Commits on Jun 30, 2016

Fixed broken link
```
Fixes #40
```
vdauwera committed on GitHub Jun 30, 2016
481aebb

Commits on Apr 25, 2016

Merge pull request #38 from broadinstitute/jg_change_preamble
```
Pointers to site in the intro
```
scottfrazer committed Apr 25, 2016
b4d7421

Commits on Apr 22, 2016

Pointers to site in the intro

geoffjentry committed Apr 22, 2016

cf1846d

Commits on Apr 19, 2016

Merge pull request #35 from mbookman/develop
```
Corrects "inputs" command reference, which moved from Cromwell to wdltool
```
scottfrazer committed Apr 19, 2016
f626822

Commits on Apr 14, 2016

Corrects "inputs" command reference, which moved from Cromwell to wdl…

…tool.

Fixes a few wdl examples, which did not work as documented.
Fixes a few instances where output did not match with the wdl.
Added output examples where omitted.

mbookman committed Apr 14, 2016

4359ce0

Commits on Mar 24, 2016

Merge pull request #32 from broadinstitute/subFunction
```
Add sub function to Spec
```
Horneth committed Mar 24, 2016
00b4629
Add sub function to Spec

Horneth committed Mar 23, 2016

997daff

Commits on Mar 8, 2016

Merge pull request #31 from broadinstitute/cjl_pullapprove_fixup
```
removed non-collaborators from .pullapprove.yml
```
cjllanwarne committed Mar 8, 2016
366e687

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