Merge pull request #403 from broadinstitute/pangolin

update pangolin and vadr containers
broadinstitute · Jan 13, 2022 · b789ef8 · b789ef8
2 parents a89269c + f362169
commit b789ef8
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Showing 4 changed files with 5 additions and 5 deletions.
diff --git a/pipes/WDL/tasks/tasks_ncbi.wdl b/pipes/WDL/tasks/tasks_ncbi.wdl
@@ -924,7 +924,7 @@ task vadr {
     File   genome_fasta
     String vadr_opts = "--glsearch -s -r --nomisc --mkey sarscov2 --lowsim5seq 6 --lowsim3seq 6 --alt_fail lowscore,insertnn,deletinn"
 
-    String docker = "quay.io/staphb/vadr:1.4-models-1.3-2"
+    String docker = "quay.io/staphb/vadr:1.4.1-models-1.3-2"
     Int    minlen = 50
     Int    maxlen = 30000
   }

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
         Boolean inference_usher=true
         Boolean update_dbs_now=false
-        String  docker = "quay.io/staphb/pangolin:3.1.17-pangolearn-2021-12-06"
+        String  docker = "quay.io/staphb/pangolin:3.1.17-pangolearn-2022-01-05"
     }
     String basename = basename(genome_fasta, ".fasta")
     command <<<
@@ -88,7 +88,7 @@ task pangolin_many_samples {
         Boolean      inference_usher=true
         Boolean      update_dbs_now=false
         String       basename
-        String       docker = "quay.io/staphb/pangolin:3.1.17-pangolearn-2021-12-06"
+        String       docker = "quay.io/staphb/pangolin:3.1.17-pangolearn-2022-01-05"
     }
     command <<<
         set -ex

diff --git a/pipes/WDL/workflows/sarscov2_illumina_full.wdl b/pipes/WDL/workflows/sarscov2_illumina_full.wdl
@@ -229,7 +229,7 @@ workflow sarscov2_illumina_full {
     call sarscov2_batch_relineage.sarscov2_batch_relineage {
       input:
         flowcell_id = flowcell_id,
-        genomes_fasta = assemble_refbased.assembly_fasta,
+        genomes_fasta = assemble_refbased.assembly_fasta, # TO DO: can this just be [passing_cat_prefilter.combined]?
         metadata_annotated_tsv = assembly_meta_tsv.combined,
         metadata_raw_tsv = assembly_meta_tsv.combined,
         min_genome_bases = min_genome_bases

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=3.1.17-pangolearn-2021-12-06
+quay.io/staphb/pangolin=3.1.17-pangolearn-2022-01-05
 nextstrain/nextclade=1.7.0