GATK 4.1.4.0 Dev (#27)

* README.md

* Update to gatk4.1

* Updated forum links in Readme

* changed ref file VM path to google bucket path

* updated import link to git tag url

* updated to GATK4.1.1.0

* minor edits

* changed import to dev for pon

* updated filter bias variable

* updated filter bias variable

* updated output variable names, removed artifact_mode from normal-normal

* changed index to idx

* removed artifact_modes

* updated import to next release: 2.4.0

* specified gatk version in readme

* Added Funcotator note to readme

* Update to gatk4.1.2.0

* updated input variable for mutect2

* correctin to input vairalbe

* correction to output variable

* corrected variable name and simplified json

* renamed input json, removed optional variables from json, updated regular mutect2 wdl with wdl version 1, updated mutect_pon wdl with wdl version 1

* removed nio wdl

* minor update

* removed comments in json because later version of cromwell throws error, replaced oncotator in json variables with funcotator

* corrections to import url for pon wdl

* mutect2 WDL and pon WDL had inconsistent input names

* mutect2 WDL and pon WDL had inconsistent input names

* added standard_runtime to pon

* add runtime structs

* add runtime structs for mergevcf

* Update mutect2_pon.wdl

minor spacing edit

* cleaned up input variables

* Update README.md

Replaced firecloud link with terra

* updated docker to 4.1.4.0, updated import url to latest release

Author: bshifaw

README.md

@@ -4,8 +4,7 @@
 Workflows for somatic short variant analysis with GATK4. 
 
 ### mutect2 :
-Implements Somatic short variant discovery using [GATK Best Practices](https://software.broadinstitute.org/gatk/best-practices/workflow).
-Note: Also provided in this repo is mutect2_nio which is a NIO supported version of the wdl.  
+Implements Somatic short variant discovery using [GATK Best Practices](https://software.broadinstitute.org/gatk/best-practices/workflow).  
 
 #### Requirements/expectations
 - Tumor bam and index
@@ -37,10 +36,10 @@ Used to validate mutect2 workflow.
 - False Positive VCF files and its index with summary  
 
 ### Software version requirements :
-- GATK4.1.2.0 
+- GATK4.1.4.0 
 
 Cromwell version support 
-- Successfully tested on v36
+- Successfully tested on v46
 
 
 ### Parameter descriptions :
@@ -104,7 +103,7 @@ By default the M2 WDL runs Funcotator for functional annotation and produce a TC
 - Runtime parameters are optimized for Broad's Google Cloud Platform implementation.
 - For help running workflows on the Google Cloud Platform or locally please
 view the following tutorial [(How to) Execute Workflows from the gatk-workflows Git Organization](https://software.broadinstitute.org/gatk/documentation/article?id=12521).
-- The following material is provided by the GATK Team. Please post any questions or concerns to one of our forum sites : [GATK](https://gatkforums.broadinstitute.org/gatk/categories/ask-the-team/) , [FireCloud](https://gatkforums.broadinstitute.org/firecloud/categories/ask-the-firecloud-team) , [WDL/Cromwell](https://gatkforums.broadinstitute.org/wdl/categories/ask-the-wdl-team).
+- The following material is provided by the GATK Team. Please post any questions or concerns to one of our forum sites : [GATK](https://gatkforums.broadinstitute.org/gatk/categories/ask-the-team/) , [Terra](https://support.terra.bio/hc/en-us/community/topics/360000500432) , [WDL/Cromwell](https://gatkforums.broadinstitute.org/wdl/categories/ask-the-wdl-team).
 - Please visit the [User Guide](https://software.broadinstitute.org/gatk/documentation/) site for further documentation on our workflows and tools.
 
 ### LICENSING :

mutect2.exome.inputs.json

@@ -0,0 +1,28 @@
+{
+  "Mutect2.gatk_docker": "broadinstitute/gatk:4.1.4.0",
+
+  "Mutect2.intervals": "gs://gatk-best-practices/somatic-b37/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.baits.interval_list",
+  "Mutect2.scatter_count": 50,
+  "Mutect2.m2_extra_args": "--downsampling-stride 20 --max-reads-per-alignment-start 6 --max-suspicious-reads-per-alignment-start 6",
+  "Mutect2.filter_funcotations": "True",
+  "Mutect2.funco_reference_version": "hg19",
+  "Mutect2.funco_data_sources_tar_gz": "gs://broad-public-datasets/funcotator/funcotator_dataSources.v1.6.20190124s.tar.gz",
+  "Mutect2.funco_transcript_selection_list": "gs://broad-public-datasets/funcotator/transcriptList.exact_uniprot_matches.AKT1_CRLF2_FGFR1.txt",
+
+  "Mutect2.ref_fasta": "gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.fasta",
+  "Mutect2.ref_dict": "gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.dict",
+  "Mutect2.ref_fai": "gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.fasta.fai",
+  "Mutect2.normal_reads": "gs://gatk-best-practices/somatic-b37/HCC1143_normal.bam",
+  "Mutect2.normal_reads_index": "gs://gatk-best-practices/somatic-b37/HCC1143_normal.bai",
+  "Mutect2.tumor_reads": "gs://gatk-best-practices/somatic-b37/HCC1143.bam",
+  "Mutect2.tumor_reads_index": "gs://gatk-best-practices/somatic-b37/HCC1143.bai",
+
+  "Mutect2.pon": "gs://gatk-best-practices/somatic-b37/Mutect2-exome-panel.vcf",
+  "Mutect2.pon_idx": "gs://gatk-best-practices/somatic-b37/Mutect2-exome-panel.vcf.idx",
+  "Mutect2.gnomad": "gs://gatk-best-practices/somatic-b37/af-only-gnomad.raw.sites.vcf",
+  "Mutect2.gnomad_idx": "gs://gatk-best-practices/somatic-b37/af-only-gnomad.raw.sites.vcf.idx",
+  "Mutect2.variants_for_contamination": "gs://gatk-best-practices/somatic-b37/small_exac_common_3.vcf",
+  "Mutect2.variants_for_contamination_idx": "gs://gatk-best-practices/somatic-b37/small_exac_common_3.vcf.idx",
+  "Mutect2.realignment_index_bundle": "gs://gatk-test-data/mutect2/Homo_sapiens_assembly38.index_bundle"
+
+}