updated to GATK4.1.1.0

mutect2-normal-normal.inputs.json

@@ -34,6 +34,6 @@
   "Mutect2NormalNormal.scatter_count": "10",
 
   "##_COMMENT4": "Docker",
-  "Mutect2NormalNormal.gatk_docker": "broadinstitute/gatk:4.0.8.1"
+  "Mutect2NormalNormal.gatk_docker": "broadinstitute/gatk:4.1.1.0"
 }
 

mutect2-normal-normal.wdl

@@ -11,7 +11,7 @@
 ## - False Positive VCF files and its index with summary
 ##
 ## Cromwell version support
-## - Successfully tested on v30
+## - Successfully tested on v36
 ##
 ## LICENSING :
 ## This script is released under the WDL source code license (BSD-3) (see LICENSE in
@@ -21,7 +21,7 @@
 ## pages at https://hub.docker.com/r/broadinstitute/* for detailed licensing information
 ## pertaining to the included programs.
 
-import "https://raw.githubusercontent.com/gatk-workflows/gatk4-somatic-snvs-indels/2.3.0/mutect2_nio.wdl" as m2
+import "https://raw.githubusercontent.com/gatk-workflows/gatk4-somatic-snvs-indels/dev/mutect2_nio.wdl" as m2
 
 workflow Mutect2NormalNormal {
 	File? intervals
@@ -37,23 +37,23 @@ workflow Mutect2NormalNormal {
 	Boolean? run_orientation_bias_filter
 	Array[String]? artifact_modes
 	File? realignment_index_bundle
-    String? realignment_extra_args
+	String? realignment_extra_args
 	String? m2_extra_args
-    String? m2_extra_filtering_args
-    Boolean? make_bamout
+	String? m2_extra_filtering_args
+	Boolean? make_bamout
 
-    File? gatk_override
-    String gatk_docker
-    Int? preemptible_attempts
+	File? gatk_override
+	String gatk_docker
+	Int? preemptible_attempts
 
-    Array[Pair[File,File]] bam_pairs = cross(bams, bams)
-    Array[Pair[File,File]] bai_pairs = cross(bais, bais)
+	Array[Pair[File,File]] bam_pairs = cross(bams, bams)
+	Array[Pair[File,File]] bai_pairs = cross(bais, bais)
 
 	scatter(n in range(length(bam_pairs))) {
 	    File tumor_bam = bam_pairs[n].left
 	    File normal_bam = bam_pairs[n].right
 	    File tumor_bai = bai_pairs[n].left
-        File normal_bai = bai_pairs[n].right
+            File normal_bai = bai_pairs[n].right
 
         if (tumor_bam != normal_bam) {
             call m2.Mutect2 {
@@ -62,10 +62,10 @@ workflow Mutect2NormalNormal {
                     ref_fasta = ref_fasta,
                     ref_fai = ref_fai,
                     ref_dict = ref_dict,
-                    tumor_bam = tumor_bam,
-                    tumor_bai = tumor_bai,
-                    normal_bam = normal_bam,
-                    normal_bai = normal_bai,
+                    tumor_reads = tumor_bam,
+                    tumor_reads_index = tumor_bai,
+                    normal_reads = normal_bam,
+                    normal_reads_index = normal_bai,
                     pon = pon,
                     scatter_count = scatter_count,
                     gnomad = gnomad,

mutect2.exome.inputs.json

@@ -1,7 +1,7 @@
 {
   "##_COMMENT1": "Runtime",
   "##Mutect2.oncotator_docker": "(optional) String?",
-  "Mutect2.gatk_docker": "broadinstitute/gatk:4.1.0.0",
+  "Mutect2.gatk_docker": "broadinstitute/gatk:4.1.1.0",
 
   "##_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",
@@ -16,10 +16,10 @@
   "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_bam": "gs://gatk-best-practices/somatic-b37/HCC1143_normal.bam",
-  "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_bai": "gs://gatk-best-practices/somatic-b37/HCC1143.bai",
+  "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",
 
   "##_COMMENT4": "Primary resources",
   "Mutect2.pon": "gs://gatk-best-practices/somatic-b37/Mutect2-exome-panel.vcf",