Haplotypecaller fix + single sample germline VC

conf/modules.config

@@ -553,23 +553,27 @@ process{
     withName: 'MERGE_HAPLOTYPECALLER' {
         ext.prefix       = {"${meta.id}.g"}
         publishDir       = [
-            enabled: !params.no_intervals,
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/haplotypecaller" },
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
     withName: 'HAPLOTYPECALLER' {
-        ext.args         = { params.joint_germline ? "-ERC GVCF" : "" }
+        ext.args         = { params.generate_gvcf ? "-ERC GVCF" : "" }
         ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}.g" : "${meta.id}_${intervals.simpleName}.g" }
         ext.when         = { params.tools && params.tools.contains('haplotypecaller') }
         publishDir       = [
-            enabled: params.no_intervals,
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/haplotypecaller"},
-            pattern: "*{vcf.gz,vcf.gz.tbi}"
+            pattern: "*{vcf.gz,vcf.gz.tbi}",
+            saveAs: { meta.num_intervals > 1 ? null : it }
         ]
     }
+
+     withName: 'FILTERVARIANTTRANCHES' {
+        ext.args         = { "--info-key CNN_1D" }
+    }
+
     withName: 'GENOTYPEGVCFS' {
         ext.when         = { params.tools && params.tools.contains('haplotypecaller') && params.joint_germline}
         publishDir       = [

conf/test.config

@@ -118,7 +118,6 @@ profiles {
         params.fasta               = params.test_data['homo_sapiens']['genome']['genome_21_fasta']
         params.intervals           = params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed']
         params.step                = 'variant_calling'
-        params.joint_germline      = true
         params.wes                 = true
 
         params.nucleotides_per_second = 20

modules.json

@@ -102,6 +102,9 @@
             "gatk4/calculatecontamination": {
                 "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
+            "gatk4/cnnscorevariants": {
+                "git_sha": "5d72500d601432f5396e9022c3a709854197db1a"
+            },
             "gatk4/createsequencedictionary": {
                 "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
@@ -111,6 +114,9 @@
             "gatk4/filtermutectcalls": {
                 "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
+            "gatk4/filtervarianttranches": {
+                "git_sha": "175ea9b7f95a0e2fd3679f7a052c6dcb60b61a6e"
+            },
             "gatk4/gatherbqsrreports": {
                 "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },