From c47c166a20e9e0fdc1f5ca685a1810607dcf58dc Mon Sep 17 00:00:00 2001 From: Danny Park Date: Tue, 19 Jul 2022 16:12:29 -0400 Subject: [PATCH 1/2] bump pangolin docker --- pipes/WDL/tasks/tasks_sarscov2.wdl | 4 ++-- requirements-modules.txt | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/pipes/WDL/tasks/tasks_sarscov2.wdl b/pipes/WDL/tasks/tasks_sarscov2.wdl index 55d93a531..b8a9a3e3a 100644 --- 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:4.1.1-pdata-1.11" + String docker = "quay.io/staphb/pangolin:4.1.2-pdata-1.12" } String basename = basename(genome_fasta, ".fasta") command <<< @@ -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-1.12" } command <<< set -ex diff --git a/requirements-modules.txt b/requirements-modules.txt index cfe7e0bec..fc3c97b2c 100644 --- 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=4.1.1-pdata-1.11 +quay.io/staphb/pangolin=4.1.2-pdata-1.12 nextstrain/nextclade=2.3.0 From 31e53b3e1eeeb96a45cc312876a1635485735b91 Mon Sep 17 00:00:00 2001 From: Danny Park Date: Tue, 13 Sep 2022 18:00:08 -0400 Subject: [PATCH 2/2] bump both pangolin and nextclade --- pipes/WDL/tasks/tasks_nextstrain.wdl | 4 ++-- pipes/WDL/tasks/tasks_sarscov2.wdl | 4 ++-- requirements-modules.txt | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl index 63286fc7e..0c03d7d50 100644 --- a/pipes/WDL/tasks/tasks_nextstrain.wdl +++ b/pipes/WDL/tasks/tasks_nextstrain.wdl @@ -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 { @@ -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 diff --git a/pipes/WDL/tasks/tasks_sarscov2.wdl b/pipes/WDL/tasks/tasks_sarscov2.wdl index b8a9a3e3a..0bdfd1327 100644 --- 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-1.12" + String docker = "quay.io/staphb/pangolin:4.1.2-pdata-1.14" } String basename = basename(genome_fasta, ".fasta") command <<< @@ -91,7 +91,7 @@ task pangolin_many_samples { String? analysis_mode Boolean update_dbs_now=false String basename - String docker = "quay.io/staphb/pangolin:4.1.2-pdata-1.12" + String docker = "quay.io/staphb/pangolin:4.1.2-pdata-1.14" } command <<< set -ex diff --git a/requirements-modules.txt b/requirements-modules.txt index fc3c97b2c..c2a5cf05c 100644 --- 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-1.12 -nextstrain/nextclade=2.3.0 +quay.io/staphb/pangolin=4.1.2-pdata-1.14 +nextstrain/nextclade=2.5.0