From bd7c76d2d803e533eb3c17376c69f2e36e6dffc5 Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Wed, 18 Sep 2024 21:53:39 -0400 Subject: [PATCH 1/2] bump nextclade and pangolin; update taxid->nextclade list --- pipes/WDL/tasks/tasks_nextstrain.wdl | 34 +++++++++++++--------------- pipes/WDL/tasks/tasks_sarscov2.wdl | 4 ++-- requirements-modules.txt | 4 ++-- 3 files changed, 20 insertions(+), 22 deletions(-) diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl index 98b1733ab..5b9764a5b 100644 --- a/pipes/WDL/tasks/tasks_nextstrain.wdl +++ b/pipes/WDL/tasks/tasks_nextstrain.wdl @@ -11,9 +11,15 @@ task taxid_to_nextclade_dataset_name { 2697049 : 'sars-cov-2', 641809 : 'flu_h1n1pdm_ha', 335341 : 'flu_h3n2_ha', + 119210 : 'flu_h3n2_ha', 518987 : 'flu_vic_ha', 208893 : 'rsv_a', 208895 : 'rsv_b', + 11234 : 'nextstrain/measles/N450/WHO-2012', + 11053 : 'nextstrain/dengue/all', + 11060 : 'nextstrain/dengue/all', + 11069 : 'nextstrain/dengue/all', + 11070 : 'nextstrain/dengue/all', 10244 : 'MPXV', 619591 : 'hMPXV' } @@ -43,13 +49,11 @@ task nextclade_one_sample { File genome_fasta File? root_sequence File? auspice_reference_tree_json - File? qc_config_json + File? pathogen_json File? gene_annotations_json - File? pcr_primers_csv - File? virus_properties String? dataset_name Int disk_size = 50 - String docker = "nextstrain/nextclade:2.14.0" + String docker = "nextstrain/nextclade:3.8.2" } String basename = basename(genome_fasta, ".fasta") command <<< @@ -76,12 +80,10 @@ task nextclade_one_sample { nextclade run \ $DATASET_ARG \ - ~{"--input-root-seq " + root_sequence} \ + ~{"--input-ref " + root_sequence} \ ~{"--input-tree " + auspice_reference_tree_json} \ - ~{"--input-qc-config " + qc_config_json} \ - ~{"--input-gene-map " + gene_annotations_json} \ - ~{"--input-pcr-primers " + pcr_primers_csv} \ - ~{"--input-virus-properties " + virus_properties} \ + ~{"--input-annotation " + gene_annotations_json} \ + ~{"--input-pathogen-json " + pathogen_json} \ --output-all=. \ --output-basename "~{basename}" \ --output-json "~{basename}".nextclade.json \ @@ -136,15 +138,13 @@ task nextclade_many_samples { Array[File]+ genome_fastas File? root_sequence File? auspice_reference_tree_json - File? qc_config_json + File? pathogen_json File? gene_annotations_json - File? pcr_primers_csv - File? virus_properties String? dataset_name String basename File? genome_ids_setdefault_blank Int disk_size = 150 - String docker = "nextstrain/nextclade:2.14.0" + String docker = "nextstrain/nextclade:3.8.2" } command <<< set -e @@ -170,12 +170,10 @@ task nextclade_many_samples { nextclade run \ $DATASET_ARG \ - ~{"--input-root-seq " + root_sequence} \ + ~{"--input-ref " + root_sequence} \ ~{"--input-tree " + auspice_reference_tree_json} \ - ~{"--input-qc-config " + qc_config_json} \ - ~{"--input-gene-map " + gene_annotations_json} \ - ~{"--input-pcr-primers " + pcr_primers_csv} \ - ~{"--input-virus-properties " + virus_properties} \ + ~{"--input-annotation " + gene_annotations_json} \ + ~{"--input-pathogen-json " + pathogen_json} \ --output-all=. \ --output-basename "~{basename}" \ --output-json "~{basename}".nextclade.json \ diff --git a/pipes/WDL/tasks/tasks_sarscov2.wdl b/pipes/WDL/tasks/tasks_sarscov2.wdl index 1d6b3341f..d4eb75ac1 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:4.3.1-pdata-1.23.1" + String docker = "quay.io/staphb/pangolin:4.3.1-pdata-1.29" } 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:4.3.1-pdata-1.23.1" + String docker = "quay.io/staphb/pangolin:4.3.1-pdata-1.29" } Int disk_size = 100 command <<< diff --git a/requirements-modules.txt b/requirements-modules.txt index e0e4ab675..ba97d6f92 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-20240318T173028Z andersenlabapps/ivar=1.3.1 -quay.io/staphb/pangolin=4.3.1-pdata-1.23.1 -nextstrain/nextclade=2.14.0 +quay.io/staphb/pangolin=4.3.1-pdata-1.29 +nextstrain/nextclade=3.8.2 From 0fd6c3b3b18074bd3c6b5a85c883550c315ab35c Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Thu, 19 Sep 2024 16:25:23 -0400 Subject: [PATCH 2/2] tag.json deprecated, long live pathogen.json --- pipes/WDL/tasks/tasks_nextstrain.wdl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl index 5b9764a5b..24d7023ea 100644 --- a/pipes/WDL/tasks/tasks_nextstrain.wdl +++ b/pipes/WDL/tasks/tasks_nextstrain.wdl @@ -71,10 +71,10 @@ task nextclade_one_sample { DATASET_ARG="--input-dataset ." python3<