[PHB Release 1.3.0] update version and docker tags (nexclade sc2, pan…

…golin, tbp-parser 1.1.7) (#296) * update version * update docker container to version 1.1.7 * update md5sum * update CI * update tag to pangolin:4.3.1-pdata-1.23.1 * update sc2 tag to 2023-12-03T12:00:00Z * update md5sum * Update task_tbp_parser.wdl --------- Co-authored-by: Sage Wright <[email protected]>
theiagen · Jan 11, 2024 · e5abd92 · e5abd92
1 parent c20eef1
commit e5abd92
Show file tree

Hide file tree

Showing 9 changed files with 19 additions and 19 deletions.
diff --git a/tasks/species_typing/task_pangolin.wdl b/tasks/species_typing/task_pangolin.wdl
@@ -6,7 +6,7 @@ task pangolin4 {
     String samplename
     Int min_length = 10000
     Float max_ambig = 0.5
-    String docker = "us-docker.pkg.dev/general-theiagen/staphb/pangolin:4.3.1-pdata-1.22"
+    String docker = "us-docker.pkg.dev/general-theiagen/staphb/pangolin:4.3.1-pdata-1.23.1"
     String? analysis_mode
     Boolean expanded_lineage=true
     Boolean skip_scorpio=false

diff --git a/tasks/species_typing/task_tbp_parser.wdl b/tasks/species_typing/task_tbp_parser.wdl
@@ -13,7 +13,7 @@ task tbp_parser {
     Int coverage_threshold = 100
     Boolean tbp_parser_debug = false
 
-    String docker = "us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:1.1.4"
+    String docker = "us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:1.1.8"
     Int disk_size = 100
     Int memory = 4
     Int cpu = 1
@@ -64,4 +64,4 @@ task tbp_parser {
     maxRetries: 3
     preemptible: 1
   }
-}
+}
diff --git a/tasks/task_versioning.wdl b/tasks/task_versioning.wdl
@@ -9,7 +9,7 @@ task version_capture {
     volatile: true
   }
   command {
-    PHB_Version="PHB v1.2.1"
+    PHB_Version="PHB v1.3.0"
     ~{default='' 'export TZ=' + timezone}
     date +"%Y-%m-%d" > TODAY
     echo "$PHB_Version" > PHB_VERSION

diff --git a/tests/workflows/theiacov/test_wf_theiacov_clearlabs.yml b/tests/workflows/theiacov/test_wf_theiacov_clearlabs.yml
@@ -320,13 +320,13 @@
     - path: miniwdl_run/call-pangolin4/work/PANGOLIN_NOTES
       md5sum: 59478efddde2191ead1b46b1f121bbc9
     - path: miniwdl_run/call-pangolin4/work/PANGO_ASSIGNMENT_VERSION
-      md5sum: edfb0c7ebdbf598df19861b650ee904a
+      md5sum: c67b44bacceaadab455401b5b0292f05
     - path: miniwdl_run/call-pangolin4/work/VERSION_PANGOLIN_ALL
-      md5sum: ef9c730f9b45d2fc284575c13fe7c920
+      md5sum: 9f9c4c00a1ceb5526bed7dc4cdb3dcfd
     - path: miniwdl_run/call-pangolin4/work/_miniwdl_inputs/0/clearlabs.medaka.consensus.fasta
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: miniwdl_run/call-pangolin4/work/clearlabs.pangolin_report.csv
-      md5sum: 58773dc8fca41e521ec7ab24df371365
+      md5sum: 45b461b9971f43a9b36b4be9c1710041
     - path: miniwdl_run/call-sc2_gene_coverage/command
       md5sum: e44c070a15a0f8d42348103b0440f691
     - path: miniwdl_run/call-sc2_gene_coverage/inputs.json

diff --git a/tests/workflows/theiacov/test_wf_theiacov_fasta.yml b/tests/workflows/theiacov/test_wf_theiacov_fasta.yml
@@ -38,7 +38,7 @@
       md5sum: 6808ca805661622ad65ae014a4b2a094
     - path: miniwdl_run/call-consensus_qc/work/_miniwdl_inputs/0/clearlabs.fasta.gz
     - path: miniwdl_run/call-nextclade/command
-      md5sum: b5ecaad831316b3bd8f066f1e71cc0a5
+      md5sum: 8d217015adda520c9fae6558584908fd
     - path: miniwdl_run/call-nextclade/inputs.json
     - path: miniwdl_run/call-nextclade/outputs.json
     - path: miniwdl_run/call-nextclade/stderr.txt
@@ -69,11 +69,11 @@
     - path: miniwdl_run/call-nextclade/work/nextclade_dataset_dir/reference.fasta
       md5sum: c7ce05f28e4ec0322c96f24e064ef55c
     - path: miniwdl_run/call-nextclade/work/nextclade_dataset_dir/sequences.fasta
-      md5sum: bb6b4e9e91304a396724bcb6344b8a5d
+      md5sum: ea475ab0a62a0a68fc3b1108fdff8a20
     - path: miniwdl_run/call-nextclade/work/nextclade_dataset_dir/tag.json
-      md5sum: 97e1309e683fbaaa839198d88cd4e2d9
+      md5sum: 7c080257b26eb528c72858e369fec68c
     - path: miniwdl_run/call-nextclade/work/nextclade_dataset_dir/tree.json
-      md5sum: 6892e6019bf88ec571b4560d66d3acb0
+      md5sum: 6b227b0aeeda07a187f5879e810879a3
     - path: miniwdl_run/call-nextclade/work/nextclade_dataset_dir/virus_properties.json
     - path: miniwdl_run/call-nextclade/work/nextclade_gene_E.translation.fasta
       md5sum: dc43b1e98245a25c142aec52b29a07df
@@ -139,12 +139,12 @@
     - path: miniwdl_run/call-pangolin4/work/PANGOLIN_NOTES
       md5sum: 71eba5c871bca955ab2a69dbd2c3c62e
     - path: miniwdl_run/call-pangolin4/work/PANGO_ASSIGNMENT_VERSION
-      md5sum: 8eb91404219a5758741f83f82e9e328d
+      md5sum: 6ee5bf9a023f7a2c3033df1d8ee93f90
     - path: miniwdl_run/call-pangolin4/work/VERSION_PANGOLIN_ALL
-      md5sum: ef9c730f9b45d2fc284575c13fe7c920
+      md5sum: 9f9c4c00a1ceb5526bed7dc4cdb3dcfd
     - path: miniwdl_run/call-pangolin4/work/_miniwdl_inputs/0/clearlabs.fasta.gz
     - path: miniwdl_run/call-pangolin4/work/fasta.pangolin_report.csv
-      md5sum: e02c65e22296686804e2be23b6d4a696
+      md5sum: 81679363ffed582650f8512794035806
     - path: miniwdl_run/call-vadr/command
       md5sum: f4ad614b7ad39f28a8145cec280a93c0
     - path: miniwdl_run/call-vadr/inputs.json

diff --git a/tests/workflows/theiacov/test_wf_theiacov_ont.yml b/tests/workflows/theiacov/test_wf_theiacov_ont.yml
@@ -222,9 +222,9 @@
     - path: miniwdl_run/call-pangolin4/work/PANGOLIN_NOTES
       md5sum: 35aa27af5fb90d54561ee9d45a3163d5
     - path: miniwdl_run/call-pangolin4/work/PANGO_ASSIGNMENT_VERSION
-      md5sum: edfb0c7ebdbf598df19861b650ee904a
+      md5sum: c67b44bacceaadab455401b5b0292f05
     - path: miniwdl_run/call-pangolin4/work/VERSION_PANGOLIN_ALL
-      md5sum: ef9c730f9b45d2fc284575c13fe7c920
+      md5sum: 9f9c4c00a1ceb5526bed7dc4cdb3dcfd
     - path: miniwdl_run/call-pangolin4/work/_miniwdl_inputs/0/ont.medaka.consensus.fasta
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: miniwdl_run/call-pangolin4/work/ont.pangolin_report.csv

diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
@@ -624,7 +624,7 @@
     - path: miniwdl_run/wdl/tasks/species_typing/task_ts_mlst.wdl
       md5sum: b83dcdc897257910bbd61868a9da49dc
     - path: miniwdl_run/wdl/tasks/task_versioning.wdl
-      md5sum: 3469cf6787f279ffa81fa50f6257fcd7
+      md5sum: cf3c274ed0ff56b743f0c0031c9966dc
     - path: miniwdl_run/wdl/tasks/taxon_id/task_gambit.wdl
       md5sum: 4e1d4f6b8085a209f9721748a0c0fef0
     - path: miniwdl_run/wdl/tasks/taxon_id/task_kraken2.wdl

diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
@@ -590,7 +590,7 @@
     - path: miniwdl_run/wdl/tasks/species_typing/task_ts_mlst.wdl
       md5sum: b83dcdc897257910bbd61868a9da49dc
     - path: miniwdl_run/wdl/tasks/task_versioning.wdl
-      md5sum: 3469cf6787f279ffa81fa50f6257fcd7
+      md5sum: cf3c274ed0ff56b743f0c0031c9966dc
     - path: miniwdl_run/wdl/tasks/taxon_id/task_gambit.wdl
       md5sum: 4e1d4f6b8085a209f9721748a0c0fef0
     - path: miniwdl_run/wdl/tasks/taxon_id/task_kraken2.wdl

diff --git a/workflows/utilities/wf_organism_parameters.wdl b/workflows/utilities/wf_organism_parameters.wdl
@@ -32,7 +32,7 @@ workflow organism_parameters {
 
   if (organism == "sars-cov-2") {
     String sc2_reference_genome = "gs://theiagen-public-files-rp/terra/augur-sars-cov-2-references/MN908947.fasta"
-    String sc2_nextclade_ds_tag = "2023-08-17T12:00:00Z"
+    String sc2_nextclade_ds_tag = "2023-12-03T12:00:00Z"
     String sc2_nextclade_ref = "MN908947"
     String sc2_nextclade_ds_name = "sars-cov-2"
     Int sc2_genome_len = 29903