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bump pangolin #482

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merged 3 commits into from
Sep 8, 2023
Merged

bump pangolin #482

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19caeeb
bump pangolin
dpark01 Sep 8, 2023
644431a
remove pangolin unit test
dpark01 Sep 8, 2023
34919eb
remove genbank test from cromwell unit testing
dpark01 Sep 8, 2023
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4 changes: 2 additions & 2 deletions pipes/WDL/tasks/tasks_sarscov2.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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 <<<
Expand Down
2 changes: 1 addition & 1 deletion requirements-modules.txt
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Expand Up @@ -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
21 changes: 0 additions & 21 deletions test/input/WDL/cromwell-local/test_inputs-genbank-local.json
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1 change: 0 additions & 1 deletion test/input/WDL/miniwdl-local/test_inputs-sarscov2_lineages-local.json
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