Merge branch 'master' into dp-augur

broadinstitute · Sep 8, 2023 · 58bdaca · 58bdaca
2 parents 1fd0a48 + 26e43f3
commit 58bdaca
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Showing 7 changed files with 10 additions and 26 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
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