broadinstitute/wdl

Commits on Apr 22, 2017

	- One "uBAM to clean BAM"; one "uBAM to HaplotypeCaller GVCF"
	- Reference-agnostic (hg38 and b37 jsons provided)
	- Can be applied to exomes instead of genomes by swapping out intervals files

vdauwera committed Apr 19, 2017

fd87f5a

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 Apr 10, 2017

Merge pull request #98 from broadinstitute/cjl_C25_update
```
Optionals methods and pair literals
```
cjllanwarne committed on GitHub Apr 10, 2017
c84ade7
Optionals methods and pair literals

cjllanwarne committed Mar 3, 2017

52e3c0c

Commits on Apr 3, 2017

Merge pull request #100 from broadinstitute/cjl_if_else_expressions
```
if then else expressions
```
cjllanwarne committed on GitHub Apr 3, 2017
3cdd802
if then else expressions

cjllanwarne committed Mar 26, 2017

61d7a84
Merge pull request #101 from broadinstitute/js_interloper_pullapprove
```
Adding jsotobroad to pullapprover members list
```
cjllanwarne committed on GitHub Apr 3, 2017
8b34c4c
Adding jsotobroad to pullapprover members list

jsotobroad committed Apr 3, 2017

7761379

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 Feb 24, 2017

checkpoint

geoffjentry committed Feb 24, 2017

7bdd8fd

Commits on Feb 22, 2017

JavaScript support for a Hermes WDL grammar (#94 )
```
* JavaScript support for a Hermes WDL grammar
```
sidoruka committed with geoffjentry Feb 22, 2017
86f4916
update grammar file to match Cromwell supported WDL version (#95 )

Horneth committed with geoffjentry Feb 22, 2017

90f3514

Commits on Feb 8, 2017

Added katevoss and alphabetized pullapprove

kshakir committed Feb 8, 2017

fa88c3b

Commits on Jan 23, 2017

Merge pull request #85 from broadinstitute/mlc_prefix_redux
```
prefix redux
```
mcovarr committed on GitHub Jan 23, 2017
35faef8
add ruchi

geoffjentry committed on GitHub Jan 23, 2017

16c6244
prefix redux

mcovarr committed Jan 17, 2017

1387e51

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 17, 2017

Merge pull request #84 from broadinstitute/mlc_join
```
prefix() proposal.  Closes broadinstitute/cromwell#375
```
mcovarr committed on GitHub Jan 17, 2017
944ebea
prefix() proposal. Closes broadinstitute/cromwell#375

mcovarr committed Jan 9, 2017

8ec60c2
Merge pull request #79 from broadinstitute/mlc_length_nee_size
```
document at length.  Closes broadinstitute/cromwell#1604
```
mcovarr committed on GitHub Jan 17, 2017
002e054

Commits on Jan 15, 2017

Add Geraldine

geoffjentry committed on GitHub Jan 15, 2017

bd10851
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

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