Merge pull request #445 from broadinstitute/pangolin

pangolin 4.1.3 / pdata 1.17
broadinstitute · Dec 15, 2022 · e2391a0 · e2391a0
2 parents e0b1f76 + ecec8a6
commit e2391a0
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Showing 3 changed files with 4 additions and 4 deletions.
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:4.1.2-pdata-1.14"
+        String  docker = "quay.io/staphb/pangolin:4.1.3-pdata-1.17"
     }
     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:4.1.2-pdata-1.14"
+        String       docker = "quay.io/staphb/pangolin:4.1.3-pdata-1.17"
     }
     Int disk_size = 100
     command <<<

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=4.1.2-pdata-1.14
+quay.io/staphb/pangolin=4.1.3-pdata-1.17
 nextstrain/nextclade=2.9.1
diff --git a/test/input/WDL/test_outputs-sarscov2_lineages-local.json b/test/input/WDL/test_outputs-sarscov2_lineages-local.json
@@ -1,5 +1,5 @@
 {
-  "sarscov2_lineages.nextclade_clade": "20C",
+  "sarscov2_lineages.nextclade_clade": "20A",
   "sarscov2_lineages.nextclade_aa_subs": "ORF1b:P314L,ORF3a:Q57H,S:D614G",
   "sarscov2_lineages.nextclade_aa_dels": "",
   "sarscov2_lineages.pango_lineage": "B.1"