Wdlupdate (#1)

* updated wdl/json to gatk4.0.1.1 release, add info for Readme

Author: bshifaw

README.md

@@ -1,2 +1,24 @@
 # somatic-snvs-indels
-Workflows for somatic short variant analysis
+
+### Purpose : 
+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) (June 2016).
+
+
+#### Requirements/expectations
+- Tumor bam and index
+- normal bam and index
+
+#### Outputs 
+- unfiltered vcf 
+- unfiltered vcf index 
+- filtered vcf 
+- filtered vcf index 
+
+### Software version requirements :
+- GATK4 or later 
+
+Cromwell version support 
+- Successfully tested on v30

mutect2.exome.inputs.json

@@ -1,29 +1,25 @@
 {
   "##_COMMENT1": "Runtime",
-  "Mutect2.gatk4_jar": "/root/gatk.jar",
-  "Mutect2.picard_jar": "gs://gatk-software/picard-2.10.0/picard.jar",
-  "Mutect2.oncotator_docker": "broadinstitute/oncotator:1.9.3.0",
-  "Mutect2.gatk_docker": "broadinstitute/gatk:4.0.0.0",
+  "Mutect2.oncotator_docker": "broadinstitute/oncotator:1.9.6.1",
+  "Mutect2.gatk_docker": "broadinstitute/gatk:4.0.1.1",
 
   "##_COMMENT2": "Workflow options",
   "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.artifact_modes": ["G/T", "C/T"],
   "##_Mutect2.m2_extra_args": "(optional) String?",
   "##_Mutect2.m2_extra_filtering_args": "(optional) String?",
-  "Mutect2.is_run_orientation_bias_filter": "True",
-  "Mutect2.is_run_oncotator": "True",
+  "Mutect2.run_orientation_bias_filter": "False",
+  "Mutect2.run_oncotator": "False",
 
   "##_COMMENT3": "Primary inputs",
   "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_fasta_index": "gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.fasta.fai",
+  "Mutect2.ref_fai": "gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.fasta.fai",
   "Mutect2.normal_bam": "gs://gatk-best-practices/somatic-b37/HCC1143_normal.bam",
-  "Mutect2.normal_bam_index": "gs://gatk-best-practices/somatic-b37/HCC1143_normal.bai",
-  "Mutect2.normal_sample_name": "HCC1143_BL",
+  "Mutect2.normal_bai": "gs://gatk-best-practices/somatic-b37/HCC1143_normal.bai",
   "Mutect2.tumor_bam": "gs://gatk-best-practices/somatic-b37/HCC1143.bam",
-  "Mutect2.tumor_bam_index": "gs://gatk-best-practices/somatic-b37/HCC1143.bai",
-  "Mutect2.tumor_sample_name": "HCC1143",
+  "Mutect2.tumor_bai": "gs://gatk-best-practices/somatic-b37/HCC1143.bai",
 
   "##_COMMENT4": "Primary resources",
   "##_Mutect2.pon": "(optional) File?",
@@ -39,30 +35,32 @@
   "##_Mutect2.sequencing_center": "(optional) String?",
   "##_Mutect2.sequence_source": "(optional) String?",
 
-  "##_COMMENT6": "Disk space",
-  "##_Mutect2.MergeVCFs.disk_space_gb": "(optional) Int?",
-  "##_Mutect2.Filter.disk_space_gb": "(optional) Int?",
-  "##_Mutect2.M2.disk_space_gb": "(optional) Int?",
-  "##_Mutect2.oncotate_m2.disk_space_gb": "(optional) Int?",
-  "##_Mutect2.SplitIntervals.disk_space_gb": "(optional) Int?",
-  "##_Mutect2.MergeBamOuts.disk_space_gb": "(optional) Int?",
-  "##_Mutect2.CollectSequencingArtifactMetrics.disk_space_gb": "(optional) Int?",
-  
-  "##_COMMENT7": "Secondary resources",
+  "##_COMMENT6": "Secondary resources",
   "##_Mutect2.MergeBamOuts.mem": "(optional) Int?",
   "##_Mutect2.SplitIntervals.mem": "(optional) Int?",
   "##_Mutect2.M2.mem": "(optional) Int?",
   "##_Mutect2.MergeVCFs.mem": "(optional) Int?",
   "##_Mutect2.oncotate_m2.mem": "(optional) Int?",
 
-  "##_COMMENT8": "Secondary resources",
+  "##_COMMENT7": "Secondary resources",
   "##_Mutect2.onco_ds_local_db_dir": "(optional) String?",
   "##_Mutect2.sequencing_center": "(optional) String?",
   "##_Mutect2.oncotate_m2.oncotator_exe": "(optional) String?",
-  "##_Mutect2.gatk4_jar_override": "(optional) File?",
+  "##_Mutect2.gatk4_override": "(optional) File?",
   "##_Mutect2.CollectSequencingArtifactMetrics.mem": "(optional) Int?",
 
-  "##_COMMENT9": "Malicious.",
+  "##_COMMENT8": "Disk space",
+  "##_Mutect2.MergeVCFs.disk_space_gb": "(optional) Int?",
+  "##_Mutect2.Filter.disk_space_gb": "(optional) Int?",
+  "##_Mutect2.M2.disk_space_gb": "(optional) Int?",
+  "##_Mutect2.M2.disk_space_gb": 100,
+  "##_Mutect2.oncotate_m2.disk_space_gb": "(optional) Int?",
+  "##_Mutect2.SplitIntervals.disk_space_gb": "(optional) Int?",
+  "##_Mutect2.MergeBamOuts.disk_space_gb": "(optional) Int?",
+  "##_Mutect2.CollectSequencingArtifactMetrics.disk_space_gb": "(optional) Int?",
+  "##_Mutect2.emergency_extra_disk": "(optional) Int?",  
+  
+  "##_COMMENT9": "Preemptibles",
   "##_Mutect2.MergeBamOuts.preemptible_attempts": "(optional) Int?",
   "Mutect2.preemptible_attempts": 3
 }