Merge pull request #79 from tmooney/anvil_walkthrough

Publish AnVIL Walkthrough

removed BamToGvcf

Dev (#19)

* Updated WDL to 1.0

* removed tasks

* add dir tasks

* added git url to import subworkflows

* removed note on FC script

* correction to import typo

shifted imports to git release 1.0.3

Wdlupdate (#12)

* removed wording for use on exomes

Wdlupdate (#7)

* Update README.md

* Update germline_single_sample_workflow.hg38.inputs.json

minor format changes

* removed scattered intervals as its not being used in the workflow, corrected haplotype_scatter_count to 50. Add comment regarding exomes intervals in Readme

* added the new HaplotypeCaller tasks.

* added a generic options

* deleted old structure

* Update README.md

minor edit

* sub_strip_path replaced by basename() because hardcoding the gs:// component makes the WDL assume too much about the platform it will run on

* removed ceil() to pass Float type as disk_size for GatherBamFiles

* Fix for splitRG task. Disk sizing now takes place within tasks.

* removed empty haplotyp map file

Wdlupdate (#7)

* Update README.md

* Update germline_single_sample_workflow.hg38.inputs.json

minor format changes

* removed scattered intervals as its not being used in the workflow, corrected haplotype_scatter_count to 50. Add comment regarding exomes intervals in Readme

* added the new HaplotypeCaller tasks.

* added a generic options

* deleted old structure

* Update README.md

minor edit

* sub_strip_path replaced by basename() because hardcoding the gs:// component makes the WDL assume too much about the platform it will run on

* removed ceil() to pass Float type as disk_size for GatherBamFiles

* Fix for splitRG task. Disk sizing now takes place within tasks.

* removed empty haplotyp map file

Wdlupdate (#4)

* Update germline_single_sample_workflow.hg38.inputs.json

* removed scattered intervals as its not being used in the workflow, corrected haplotype_scatter_count to 50. Add comment regarding exomes intervals in Readme

* added the new HaplotypeCaller tasks.

* added a generic options

* deleted old structure

* sub_strip_path replaced by basename() because hardcoding the gs:// component makes the WDL assume too much about the platform it will run on