broadinstitute/wdl

Commits on Apr 21, 2017

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
Update README.md

vdauwera committed Apr 21, 2017

10bd78c

Commits on Apr 19, 2017

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

Update supported GOTC single-sample and add pipeline documentation

vdauwera committed Apr 11, 2017

2d6595e
Update GOTC single-sample workflow to functional equivalence version

vdauwera committed Apr 11, 2017

a887782

Commits on Mar 6, 2017

Merge pull request #88 from broadinstitute/gvda_standalone_calling_steps
```
Standalone variant calling steps + joint discovery
```
vdauwera committed on GitHub Mar 6, 2017
7e6f95b

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

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

GA4GH Tool Execution Challenge Phase 1

vdauwera committed Feb 27, 2017

b57db7e

Commits on Jan 22, 2017

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

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

Merge pull request #82 from broadinstitute/gvda_trivial_bam_manipulation
```
WDLs for trivial bam manipulation
```
vdauwera committed on GitHub Jan 21, 2017
9f7bfa8

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

Merge pull request #80 from broadinstitute/gvda_subset_scatter_intervals
```
Add script to generate subsets of scatter intervals from master list
```
vdauwera committed on GitHub Jan 15, 2017
db70b71
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

Merge pull request #81 from broadinstitute/gvda_supported_dir_readme_…
```
…plus_generic_options

New directory for DSDE-supported-but-not-prod WDLs
```
vdauwera committed on GitHub Jan 13, 2017
2cdd412
New directory for supported-but-not-prod WDLs; includes README and a …
```
…generic options file
```
vdauwera committed Jan 8, 2017
8c9daf3

Commits on Oct 27, 2016

Merge pull request #69 from broadinstitute/jt_readme
```
Fix URL in Readme
```
vdauwera committed on GitHub Oct 27, 2016
28d4997

Commits on Oct 12, 2016

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 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

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 #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

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