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bump pangolin to 4.1.2-1.14 and nextclade to 2.5.0 #434

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merged 3 commits into from
Sep 14, 2022
Merged

bump pangolin to 4.1.2-1.14 and nextclade to 2.5.0 #434

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c47c166
bump pangolin docker
dpark01 Jul 19, 2022
31e53b3
bump both pangolin and nextclade
dpark01 Sep 13, 2022
f2271ae
Merge branch 'master' into pangolin
dpark01 Sep 14, 2022
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4 changes: 2 additions & 2 deletions pipes/WDL/tasks/tasks_nextstrain.wdl
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Expand Up @@ -13,7 +13,7 @@ task nextclade_one_sample {
File? pcr_primers_csv
File? virus_properties
String? dataset_name
String docker = "nextstrain/nextclade:2.3.0"
String docker = "nextstrain/nextclade:2.5.0"
}
String basename = basename(genome_fasta, ".fasta")
command {
Expand Down Expand Up @@ -98,7 +98,7 @@ task nextclade_many_samples {
String? dataset_name
String basename
File? genome_ids_setdefault_blank
String docker = "nextstrain/nextclade:2.3.0"
String docker = "nextstrain/nextclade:2.5.0"
}
command <<<
set -e
Expand Down
4 changes: 2 additions & 2 deletions pipes/WDL/tasks/tasks_sarscov2.wdl
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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:4.1.1-pdata-1.11"
String docker = "quay.io/staphb/pangolin:4.1.2-pdata-1.14"
}
String basename = basename(genome_fasta, ".fasta")
command <<<
Expand Down Expand Up @@ -91,7 +91,7 @@ task pangolin_many_samples {
String? analysis_mode
Boolean update_dbs_now=false
String basename
String docker = "quay.io/staphb/pangolin:4.1.1-pdata-1.11"
String docker = "quay.io/staphb/pangolin:4.1.2-pdata-1.14"
}
command <<<
set -ex
Expand Down
4 changes: 2 additions & 2 deletions 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=4.1.1-pdata-1.11
nextstrain/nextclade=2.3.0
quay.io/staphb/pangolin=4.1.2-pdata-1.14
nextstrain/nextclade=2.5.0