diff --git a/pipes/WDL/tasks/tasks_interhost.wdl b/pipes/WDL/tasks/tasks_interhost.wdl
index 38f64ad66..14598f19c 100644
--- a/pipes/WDL/tasks/tasks_interhost.wdl
+++ b/pipes/WDL/tasks/tasks_interhost.wdl
@@ -168,6 +168,9 @@ task beast {
   output {
     File        beast_log    = glob("*.log")[0]
     Array[File] trees        = glob("*.trees")
+    Array[File] ops          = glob("*.ops")
+    Array[File] rates        = glob("*.rates")
+    Array[File] root         = glob("*.root")
     File        beast_stdout = stdout()
   }
 
diff --git a/pipes/WDL/tasks/tasks_ncbi.wdl b/pipes/WDL/tasks/tasks_ncbi.wdl
index bcd46bc5c..7726266d0 100644
--- a/pipes/WDL/tasks/tasks_ncbi.wdl
+++ b/pipes/WDL/tasks/tasks_ncbi.wdl
@@ -60,7 +60,7 @@ task download_annotations {
   >>>
 
   output {
-    File        combined_fasta   = "~{combined_out_prefix}.fasta"
+    File        combined_fasta   = "combined/~{combined_out_prefix}.fasta"
     Array[File] genomes_fasta    = glob("*.fasta")
     Array[File] features_tbl     = glob("*.tbl")
     String      viralngs_version = read_string("VERSION")
diff --git a/pipes/WDL/tasks/tasks_sarscov2.wdl b/pipes/WDL/tasks/tasks_sarscov2.wdl
index 041a6f430..cb9866ec3 100644
--- a/pipes/WDL/tasks/tasks_sarscov2.wdl
+++ b/pipes/WDL/tasks/tasks_sarscov2.wdl
@@ -10,7 +10,7 @@ task pangolin_one_sample {
         Float?  max_ambig
         String? analysis_mode
         Boolean update_dbs_now=false
-        String  docker = "quay.io/staphb/pangolin:4.2-pdata-1.18.1.1"
+        String  docker = "quay.io/staphb/pangolin:4.3.1-pdata-1.22"
     }
     String basename = basename(genome_fasta, ".fasta")
     Int disk_size = 50
@@ -93,7 +93,7 @@ task pangolin_many_samples {
         String?      analysis_mode
         Boolean      update_dbs_now=false
         String       basename
-        String       docker = "quay.io/staphb/pangolin:4.2-pdata-1.18.1.1"
+        String       docker = "quay.io/staphb/pangolin:4.3.1-pdata-1.22"
     }
     Int disk_size = 100
     command <<<
diff --git a/pipes/WDL/workflows/beast_gpu.wdl b/pipes/WDL/workflows/beast_gpu.wdl
index 10c428ca3..1fef20063 100644
--- a/pipes/WDL/workflows/beast_gpu.wdl
+++ b/pipes/WDL/workflows/beast_gpu.wdl
@@ -13,6 +13,9 @@ workflow beast_gpu {
     output {
         File        beast_log    = beast.beast_log
         Array[File] trees        = beast.trees
+        Array[File] ops          = beast.ops
+        Array[File] rates        = beast.rates
+        Array[File] root         = beast.root
         String      beast_stdout = beast.beast_stdout
     }
 }
diff --git a/requirements-modules.txt b/requirements-modules.txt
index f2dcc6cd1..b20c89a98 100644
--- a/requirements-modules.txt
+++ b/requirements-modules.txt
@@ -7,5 +7,5 @@ broadinstitute/beast-beagle-cuda=1.10.5pre
 broadinstitute/ncbi-tools=2.10.7.10
 nextstrain/base=build-20211012T204409Z
 andersenlabapps/ivar=1.3.1
-quay.io/staphb/pangolin=4.2-pdata-1.18.1.1
+quay.io/staphb/pangolin=4.3.1-pdata-1.22
 nextstrain/nextclade=2.12.0
diff --git a/test/input/WDL/cromwell-local/test_inputs-genbank-local.json b/test/input/WDL/cromwell-local/test_inputs-genbank-local.json
deleted file mode 100644
index e6af063fe..000000000
--- a/test/input/WDL/cromwell-local/test_inputs-genbank-local.json
+++ /dev/null
@@ -1,21 +0,0 @@
-{
-  "genbank.molType": "cRNA",
-  "genbank.coverage_table": "test/input/genbank/coverage-ma_mgh.txt",
-  "genbank.alignments_bams": [],
-  "genbank.reference_accessions": ["MN908947.3"],
-  "genbank.sequencingTech": "Illumina NovaSeq",
-  "genbank.biosample_attributes": "test/input/genbank/sars-cov-2_attributes_updated.txt",
-  "genbank.prep_genbank.assembly_method": "placeholder assembly software",
-  "genbank.prep_genbank.assembly_method_version": "5.4.3.2.1",
-  "genbank.comment": "this is only a test -- DO NOT SUBMIT to NCBI",
-  "genbank.author_list": "Odia,Ikponmwosa, Ehaine,Philomena, Oguzie,Judith,U. Siddle,Katherine,J. Mehta,Samar, Barnes,Kayla,M. Winnicki,Sarah,M. Brehio,Patrick, Shah,Rickey,R. Chak,Bridget, Yozwiak,Nathan, Amao,Adebayo, Nosamiefan,Iguosadolo, Birren,Bruce,W. Park,Daniel,J. Folarin,Onikepe, Okokhere,Peter, Sabeti,Pardis,C. Happi,Christian,T.",
-  "genbank.author_sbt_defaults_yaml": "test/input/genbank/default_sbt_values.yaml",
-  "genbank.author_sbt_j2_template": "test/input/genbank/author_template.sbt.j2",
-  "genbank.assemblies_fasta": [
-    "test/input/MA_MGH_00003.fasta",
-    "test/input/MA_MGH_00004.fasta",
-    "test/input/MA_MGH_00005.fasta"
-  ],
-  "genbank.email_address": "viral-ngs@broadinstitute.org"
-}
-
diff --git a/test/input/WDL/miniwdl-local/test_inputs-sarscov2_lineages-local.json b/test/input/WDL/miniwdl-local/test_inputs-sarscov2_lineages-local.json
deleted file mode 120000
index 59916f987..000000000
--- a/test/input/WDL/miniwdl-local/test_inputs-sarscov2_lineages-local.json
+++ /dev/null
@@ -1 +0,0 @@
-../test_inputs-sarscov2_lineages-local.json
\ No newline at end of file