Merge pull request #203 from theiagen/kgl-version-update

Update version and SC2 references
theiagen · Dec 30, 2022 · 031037f · 031037f
2 parents 8f0871a + e723cef
commit 031037f
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Showing 11 changed files with 54 additions and 54 deletions.
diff --git a/tasks/task_taxonID.wdl b/tasks/task_taxonID.wdl
@@ -144,7 +144,7 @@ task pangolin4 {
     String samplename
     Int min_length = 10000
     Float max_ambig = 0.5
-    String docker = "staphb/pangolin:4.1.2-pdata-1.12"
+    String docker = "staphb/pangolin:4.1.3-pdata-1.17"
     String? analysis_mode
     Boolean expanded_lineage=true
     Boolean skip_scorpio=false

diff --git a/tasks/task_versioning.wdl b/tasks/task_versioning.wdl
@@ -9,7 +9,7 @@ task version_capture {
     volatile: true
   }
   command <<<
-    PHVG_Version="PHVG 2.3.0-dev"
+    PHVG_Version="PHVG 2.3.0"
     ~{default='' 'export TZ=' + timezone}
     date +"%Y-%m-%d" > TODAY
     echo $PHVG_Version > PHVG_VERSION

diff --git a/tests/workflows/test_clearlabs.yml b/tests/workflows/test_clearlabs.yml
@@ -212,7 +212,7 @@
     - path: miniwdl_run/call-ncbi_scrub_se/work/r1.fastq.clean
       md5sum: 033e7bdb8c34ed0df11bf9f604addb54
     - path: miniwdl_run/call-nextclade_one_sample/command
-      md5sum: 0efc55d76a6c1ad4017d18c6149c6eab
+      md5sum: 9c7cb5f727c215afd966b5a680b3d201
     - path: miniwdl_run/call-nextclade_one_sample/inputs.json
       contains: ["dataset_name", "dataset_tag", "genome_fasta"]
     - path: miniwdl_run/call-nextclade_one_sample/outputs.json
@@ -229,11 +229,11 @@
     - path: miniwdl_run/call-nextclade_one_sample/work/clearlabs.medaka.consensus.nextclade.auspice.json
     - path: miniwdl_run/call-nextclade_one_sample/work/clearlabs.medaka.consensus.nextclade.json
     - path: miniwdl_run/call-nextclade_one_sample/work/clearlabs.medaka.consensus.nextclade.tsv
-      md5sum: 14862320a34113ff363c514fd72cd117
+      md5sum: b1c583d5e2902d442501a8b9d1853508
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade.aligned.fasta
       md5sum: 0961549fb82f231ca3d27b07d68dc18c
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade.csv
-      md5sum: 28413fd8f7810df99f0bbfdbbcf70061
+      md5sum: 6fdc3589a1e9a110286cbd9f4a781213
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade.errors.csv
       md5sum: be674cbaf42271c6555b69e1d069447b
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade.insertions.csv
@@ -246,7 +246,7 @@
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade_dataset_dir/reference.fasta
       md5sum: c7ce05f28e4ec0322c96f24e064ef55c
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade_dataset_dir/sequences.fasta
-      md5sum: 63d9c2592b5e3adb466e2f57f1efb7d2
+      md5sum: 154d65f2491793dbb5e74b14a55309b4
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade_dataset_dir/tag.json
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade_dataset_dir/tree.json
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade_dataset_dir/virus_properties.json
@@ -294,7 +294,7 @@
     - path: miniwdl_run/call-nextclade_output_parser_one_sample/work/_miniwdl_inputs/0/clearlabs.medaka.consensus.nextclade.tsv
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: miniwdl_run/call-nextclade_output_parser_one_sample/work/input.tsv
-      md5sum: 14862320a34113ff363c514fd72cd117
+      md5sum: b1c583d5e2902d442501a8b9d1853508
     - path: miniwdl_run/call-pangolin4/command
       md5sum: 6dde0f23a53493f2a5c04cbd99313e46
     - path: miniwdl_run/call-pangolin4/inputs.json
@@ -314,15 +314,15 @@
     - path: miniwdl_run/call-pangolin4/work/PANGOLIN_LINEAGE
       md5sum: 717da6cd0df2d2f1d00461f3498aaca9
     - path: miniwdl_run/call-pangolin4/work/PANGOLIN_NOTES
-      md5sum: 90d3fe0732810e69b2e7a8aa42772bfa
+      md5sum: 0d654329677a43e9626ea3921b924662
     - path: miniwdl_run/call-pangolin4/work/PANGO_ASSIGNMENT_VERSION
-      md5sum: c3e2bf00d4a82d39cc9137f5c2a6764b
+      md5sum: 4e434d75ffecbd1669b89698d0f74d9e
     - path: miniwdl_run/call-pangolin4/work/VERSION_PANGOLIN_ALL
-      md5sum: 197cb8ecf4898fbd589243cf65100cc1
+      md5sum: 610311d600672ebc0fb9c138cab9945a
     - 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: 1ee67e087079b551da5d02345bbf5ad0
+      md5sum: 8f98ee098c10003b1a04cb13493aec78
     - path: miniwdl_run/call-sc2_gene_coverage/command
       md5sum: 7090d929e3e59de1b4799d44824bf1d3
     - path: miniwdl_run/call-sc2_gene_coverage/inputs.json
@@ -486,11 +486,11 @@
     - path: miniwdl_run//wdl/tasks/task_sc2_gene_coverage.wdl
       md5sum: e8310700d96d98cd16f4859f61dd179f
     - path: miniwdl_run/wdl/tasks/task_taxonID.wdl
-      md5sum: b027e1671929931f9c2ab4ba38696139
+      md5sum: ac535cb1d1a51a5ca578cb26714a49a7
     - path: miniwdl_run/wdl/tasks/task_versioning.wdl
-      md5sum: d55d15a9f120059591c23274be99a956
+      md5sum: 27d436979d253be67940a84696c5b77b
     - path: miniwdl_run/wdl/workflows/wf_theiacov_clearlabs.wdl
-      md5sum: 437b7b62e64dcb8cbf86cf3da147b4d0
+      md5sum: 46804457134e58b17493b1b408219e25
     - path: miniwdl_run/inputs.json
       contains: ["theiacov_clearlabs", "samplename", "primer_bed"]
     - path: miniwdl_run/outputs.json

diff --git a/tests/workflows/test_illumina_pe.yml b/tests/workflows/test_illumina_pe.yml
@@ -84,7 +84,7 @@
     - path: miniwdl_run/call-consensus_qc/work/_miniwdl_inputs/0/SRR13687078.ivar.consensus.fasta
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: miniwdl_run/call-nextclade_one_sample/command
-      md5sum: e602be649dd0e6fee5547e5bd4623046
+      md5sum: bd2591221e476dcf05a436e642bab99f
     - path: miniwdl_run/call-nextclade_one_sample/inputs.json
       contains: ["dataset_name", "genome_fasta", "SRR13687078"]
     - path: miniwdl_run/call-nextclade_one_sample/outputs.json
@@ -99,13 +99,13 @@
     - path: miniwdl_run/call-nextclade_one_sample/work/SRR13687078.ivar.consensus.nextclade.auspice.json
     - path: miniwdl_run/call-nextclade_one_sample/work/SRR13687078.ivar.consensus.nextclade.json
     - path: miniwdl_run/call-nextclade_one_sample/work/SRR13687078.ivar.consensus.nextclade.tsv
-      md5sum: 396d029129547116c3095245e8458be4
+      md5sum: 3b7bea85bf79f45e9319251540a7bab7
     - path: miniwdl_run/call-nextclade_one_sample/work/_miniwdl_inputs/0/SRR13687078.ivar.consensus.fasta
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade.aligned.fasta
       md5sum: fd4752351ef527736a7cae798f4d8114
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade.csv
-      md5sum: f469e6bc20d0ed851379d31bc192fa9d
+      md5sum: 54b511787cc3f052256d8f4cb4fca26e
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade.errors.csv
       md5sum: 760bf7f9d66794168719b1c5c67994b3
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade.insertions.csv
@@ -118,7 +118,7 @@
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade_dataset_dir/reference.fasta
       md5sum: c7ce05f28e4ec0322c96f24e064ef55c
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade_dataset_dir/sequences.fasta
-      md5sum: 63d9c2592b5e3adb466e2f57f1efb7d2
+      md5sum: 154d65f2491793dbb5e74b14a55309b4
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade_dataset_dir/tag.json
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade_dataset_dir/tree.json
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade_dataset_dir/virus_properties.json
@@ -166,7 +166,7 @@
     - path: miniwdl_run/call-nextclade_output_parser_one_sample/work/_miniwdl_inputs/0/SRR13687078.ivar.consensus.nextclade.tsv
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: miniwdl_run/call-nextclade_output_parser_one_sample/work/input.tsv
-      md5sum: 396d029129547116c3095245e8458be4
+      md5sum: 3b7bea85bf79f45e9319251540a7bab7
     - path: miniwdl_run/call-pangolin4/command
       md5sum: a175cc8e19c30ab61c88d24fe694919b
     - path: miniwdl_run/call-pangolin4/inputs.json
@@ -188,11 +188,11 @@
     - path: miniwdl_run/call-pangolin4/work/PANGOLIN_NOTES
       md5sum: c72695b331cf7d87edfebc08f903b081
     - path: miniwdl_run/call-pangolin4/work/PANGO_ASSIGNMENT_VERSION
-      md5sum: c3e2bf00d4a82d39cc9137f5c2a6764b
+      md5sum: 4e434d75ffecbd1669b89698d0f74d9e
     - path: miniwdl_run/call-pangolin4/work/SRR13687078.pangolin_report.csv
-      md5sum: 891059ed33581c032082d555ccf7b422
+      md5sum: 47c00bf9759206ee2867357501bed615
     - path: miniwdl_run/call-pangolin4/work/VERSION_PANGOLIN_ALL
-      md5sum: 197cb8ecf4898fbd589243cf65100cc1
+      md5sum: 610311d600672ebc0fb9c138cab9945a
     - path: miniwdl_run/call-pangolin4/work/_miniwdl_inputs/0/SRR13687078.ivar.consensus.fasta
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: miniwdl_run/call-primer_trim/command
@@ -602,13 +602,13 @@
     - path: miniwdl_run/wdl/tasks/task_sc2_gene_coverage.wdl
       md5sum: e8310700d96d98cd16f4859f61dd179f
     - path: miniwdl_run/wdl/tasks/task_taxonID.wdl
-      md5sum: b027e1671929931f9c2ab4ba38696139
+      md5sum: ac535cb1d1a51a5ca578cb26714a49a7
     - path: miniwdl_run/wdl/tasks/task_versioning.wdl
-      md5sum: d55d15a9f120059591c23274be99a956
+      md5sum: 27d436979d253be67940a84696c5b77b
     - path: miniwdl_run/wdl/workflows/wf_read_QC_trim.wdl
       md5sum: 9769f7ff548537ed7d36c5d0df445416
     - path: miniwdl_run/wdl/workflows/wf_theiacov_illumina_pe.wdl
-      md5sum: 9efc4b697aa5b57d80146a8c45eba447
+      md5sum: 6406571dc8f4da9635e78938e02bc389
     - path: miniwdl_run/inputs.json
       contains: ["theiacov_illumina_pe", "samplename", "primer_bed"]
     - path: miniwdl_run/outputs.json

diff --git a/tests/workflows/test_illumina_se.yml b/tests/workflows/test_illumina_se.yml
@@ -83,7 +83,7 @@
     - path: miniwdl_run/call-consensus_qc/work/_miniwdl_inputs/0/ERR6319327.ivar.consensus.fasta
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: miniwdl_run/call-nextclade_one_sample/command
-      md5sum: 74165cca8dc615b290f2ceeb9f8eff70
+      md5sum: 2d49c11b52b47763fcbee9ee6b5abbc8
     - path: miniwdl_run/call-nextclade_one_sample/inputs.json
       contains: ["dataset_name", "genome_fasta", "ERR6319327"]
     - path: miniwdl_run/call-nextclade_one_sample/outputs.json
@@ -96,15 +96,15 @@
     - path: miniwdl_run/call-nextclade_one_sample/work/ERR6319327.ivar.consensus.nextclade.auspice.json
     - path: miniwdl_run/call-nextclade_one_sample/work/ERR6319327.ivar.consensus.nextclade.json
     - path: miniwdl_run/call-nextclade_one_sample/work/ERR6319327.ivar.consensus.nextclade.tsv
-      md5sum: feb5a815a261ac9dd1b1a14f0a09f1c0
+      md5sum: 72e5e5425b962adb8a74acb337b104f9
     - path: miniwdl_run/call-nextclade_one_sample/work/NEXTCLADE_VERSION
       md5sum: c742549fbfacb35776d8908e1b828b82
     - path: miniwdl_run/call-nextclade_one_sample/work/_miniwdl_inputs/0/ERR6319327.ivar.consensus.fasta
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade.aligned.fasta
       md5sum: ddab97b3f5a3dda718c107447c90dfaf
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade.csv
-      md5sum: e3d7018543bc976a4f9c4a8036d6029b
+      md5sum: 2d2a57de95edb4d738e8141a221645fb
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade.errors.csv
       md5sum: 03237c467785ee9f0574c38264a4f7ed
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade.insertions.csv
@@ -117,7 +117,7 @@
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade_dataset_dir/reference.fasta
       md5sum: c7ce05f28e4ec0322c96f24e064ef55c
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade_dataset_dir/sequences.fasta
-      md5sum: 63d9c2592b5e3adb466e2f57f1efb7d2
+      md5sum: 154d65f2491793dbb5e74b14a55309b4
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade_dataset_dir/tag.json
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade_dataset_dir/tree.json
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade_dataset_dir/virus_properties.json
@@ -166,7 +166,7 @@
     - path: miniwdl_run/call-nextclade_output_parser_one_sample/work/_miniwdl_inputs/0/ERR6319327.ivar.consensus.nextclade.tsv
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: miniwdl_run/call-nextclade_output_parser_one_sample/work/input.tsv
-      md5sum: feb5a815a261ac9dd1b1a14f0a09f1c0
+      md5sum: 72e5e5425b962adb8a74acb337b104f9
     - path: miniwdl_run/call-pangolin4/command
       md5sum: 46f28e89ee8bf39282f6ae06cf3ec4a1
     - path: miniwdl_run/call-pangolin4/inputs.json
@@ -180,19 +180,19 @@
       contains: ["wdl", "theiacov_illumina_se", "pangolin", "done"]
     - path: miniwdl_run/call-pangolin4/work/DATE
     - path: miniwdl_run/call-pangolin4/work/ERR6319327.pangolin_report.csv
-      md5sum: d6516ab3a3720040ef2098617442e519
+      md5sum: 29a1f778b2387ddb31aedf2627e2c895
     - path: miniwdl_run/call-pangolin4/work/EXPANDED_LINEAGE
       md5sum: 2430b919e9b5f418c6a13add9d3c1db8
     - path: miniwdl_run/call-pangolin4/work/PANGOLIN_CONFLICTS
       md5sum: 30565a8911a6bb487e3745c0ea3c8224
     - path: miniwdl_run/call-pangolin4/work/PANGOLIN_LINEAGE
       md5sum: 2430b919e9b5f418c6a13add9d3c1db8
     - path: miniwdl_run/call-pangolin4/work/PANGOLIN_NOTES
-      md5sum: 0b1f8fb5b938fe71631f61234cbf7ab3
+      md5sum: 26668c8b0624d99676391b00c9775d2a
     - path: miniwdl_run/call-pangolin4/work/PANGO_ASSIGNMENT_VERSION
-      md5sum: c3e2bf00d4a82d39cc9137f5c2a6764b
+      md5sum: 4e434d75ffecbd1669b89698d0f74d9e
     - path: miniwdl_run/call-pangolin4/work/VERSION_PANGOLIN_ALL
-      md5sum: 197cb8ecf4898fbd589243cf65100cc1
+      md5sum: 610311d600672ebc0fb9c138cab9945a
     - path: miniwdl_run/call-pangolin4/work/_miniwdl_inputs/0/ERR6319327.ivar.consensus.fasta
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: miniwdl_run/call-primer_trim/command
@@ -512,13 +512,13 @@
     - path: miniwdl_run/wdl/tasks/task_sc2_gene_coverage.wdl
       md5sum: e8310700d96d98cd16f4859f61dd179f
     - path: miniwdl_run/wdl/tasks/task_taxonID.wdl
-      md5sum: b027e1671929931f9c2ab4ba38696139
+      md5sum: ac535cb1d1a51a5ca578cb26714a49a7
     - path: miniwdl_run/wdl/tasks/task_versioning.wdl
-      md5sum: d55d15a9f120059591c23274be99a956
+      md5sum: 27d436979d253be67940a84696c5b77b
     - path: miniwdl_run/wdl/workflows/wf_read_QC_trim_se.wdl
       md5sum: eb4170a3da9d95720b5403dd3d5e5d87
     - path: miniwdl_run/wdl/workflows/wf_theiacov_illumina_se.wdl
-      md5sum: 10efca1451aa24cf50780573d9f47441
+      md5sum: f671b5892d161d806c72469f82b123fb
     - path: miniwdl_run/inputs.json
       contains: ["theiacov_illumina_se", "samplename", "primer_bed"]
     - path: miniwdl_run/outputs.json

diff --git a/tests/workflows/test_ont.yml b/tests/workflows/test_ont.yml
@@ -208,7 +208,7 @@
     - path: miniwdl_run/call-ncbi_scrub_se/work/r1.fastq.clean
       md5sum: 2cf5f8defc05395fecd10c68865f9ae3
     - path: miniwdl_run/call-nextclade_one_sample/command
-      md5sum: a509a0893a398650ce830987f13bbbe4
+      md5sum: dbb8b44b834e08b728c9dc89de3c3b71
     - path: miniwdl_run/call-nextclade_one_sample/inputs.json
       contains: ["dataset_name", "dataset_tag", "genome_fasta"]
     - path: miniwdl_run/call-nextclade_one_sample/outputs.json
@@ -225,7 +225,7 @@
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade.aligned.fasta
       md5sum: 8210832b44151b6c50644e6541e60bec
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade.csv
-      md5sum: 4c25311e2225f3caac4b14277fbcbab3
+      md5sum: 58244260d4d8e389ecd0682616516c56
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade.errors.csv
       md5sum: c903ba15cb277fc61f3e5f1d0a359ecb
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade.insertions.csv
@@ -235,11 +235,11 @@
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade_dataset_dir/primers.csv
       md5sum: 5990c3483bf66ce607aeb90a44e7ef2e
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade_dataset_dir/qc.json
-      md5sum: 58753d666c02596c2fdaf31b2efe2a5d
+      md5sum: 518c01e982a20712d67fafb5c5fc953c
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade_dataset_dir/reference.fasta
       md5sum: c7ce05f28e4ec0322c96f24e064ef55c
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade_dataset_dir/sequences.fasta
-      md5sum: 63d9c2592b5e3adb466e2f57f1efb7d2
+      md5sum: 154d65f2491793dbb5e74b14a55309b4
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade_dataset_dir/tag.json
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade_dataset_dir/tree.json
     - path: miniwdl_run/call-nextclade_one_sample/work/nextclade_dataset_dir/virus_properties.json
@@ -270,7 +270,7 @@
     - path: miniwdl_run/call-nextclade_one_sample/work/ont.medaka.consensus.nextclade.auspice.json
     - path: miniwdl_run/call-nextclade_one_sample/work/ont.medaka.consensus.nextclade.json
     - path: miniwdl_run/call-nextclade_one_sample/work/ont.medaka.consensus.nextclade.tsv
-      md5sum: 5fc739d400d9684b6342e2fec33ce584
+      md5sum: a249e397f604cf59fe38d804d90970ab
     - path: miniwdl_run/call-nextclade_output_parser_one_sample/command
       md5sum: 9aa44f805c73bbe782a3c8328a83cefb
     - path: miniwdl_run/call-nextclade_output_parser_one_sample/inputs.json
@@ -291,7 +291,7 @@
     - path: miniwdl_run/call-nextclade_output_parser_one_sample/work/_miniwdl_inputs/0/ont.medaka.consensus.nextclade.tsv
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: miniwdl_run/call-nextclade_output_parser_one_sample/work/input.tsv
-      md5sum: 5fc739d400d9684b6342e2fec33ce584
+      md5sum: a249e397f604cf59fe38d804d90970ab
     - path: miniwdl_run/call-pangolin4/command
       md5sum: a39d22f657432d05a5670ce6adc8bf07
     - path: miniwdl_run/call-pangolin4/inputs.json
@@ -313,13 +313,13 @@
     - path: miniwdl_run/call-pangolin4/work/PANGOLIN_NOTES
       md5sum: 35aa27af5fb90d54561ee9d45a3163d5
     - path: miniwdl_run/call-pangolin4/work/PANGO_ASSIGNMENT_VERSION
-      md5sum: c3e2bf00d4a82d39cc9137f5c2a6764b
+      md5sum: 4e434d75ffecbd1669b89698d0f74d9e
     - path: miniwdl_run/call-pangolin4/work/VERSION_PANGOLIN_ALL
-      md5sum: 197cb8ecf4898fbd589243cf65100cc1
+      md5sum: 610311d600672ebc0fb9c138cab9945a
     - 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
-      md5sum: 3ce92c7f791eb0d1331fb49cc07ed0b9
+      md5sum: b7b9dcced52783d5153dc469971be4fe
     - path: miniwdl_run/call-read_filtering/command
       md5sum: 5a9e0fdba76808aef9f652244d355675
     - path: miniwdl_run/call-read_filtering/inputs.json
@@ -494,11 +494,11 @@
     - path: miniwdl_run/wdl/tasks/task_sc2_gene_coverage.wdl
       md5sum: e8310700d96d98cd16f4859f61dd179f
     - path: miniwdl_run/wdl/tasks/task_taxonID.wdl
-      md5sum: b027e1671929931f9c2ab4ba38696139
+      md5sum: ac535cb1d1a51a5ca578cb26714a49a7
     - path: miniwdl_run/wdl/tasks/task_versioning.wdl
-      md5sum: d55d15a9f120059591c23274be99a956
+      md5sum: 27d436979d253be67940a84696c5b77b
     - path: miniwdl_run/wdl/workflows/wf_theiacov_ont.wdl
-      md5sum: b543819a4cdef1cc9eb1b6baa192629c
+      md5sum: c7912b6c992ff5633c7e72afeb8e7e72
     - path: miniwdl_run/inputs.json
       contains: ["theiacov_ont", "samplename", "primer_bed"]
     - path: miniwdl_run/outputs.json

diff --git a/workflows/wf_theiacov_clearlabs.wdl b/workflows/wf_theiacov_clearlabs.wdl
@@ -21,7 +21,7 @@ workflow theiacov_clearlabs {
     File primer_bed
     Int normalise = 20000
     String nextclade_dataset_reference = "MN908947"
-    String nextclade_dataset_tag = "2022-09-27T12:00:00Z"
+    String nextclade_dataset_tag = "2022-12-14T12:00:00Z"
     String medaka_docker = "quay.io/staphb/artic-ncov2019:1.3.0-medaka-1.4.3"
     String? nextclade_dataset_name
     File? reference_genome

diff --git a/workflows/wf_theiacov_fasta.wdl b/workflows/wf_theiacov_fasta.wdl
@@ -15,7 +15,7 @@ workflow theiacov_fasta {
     String seq_method
     String input_assembly_method
     String nextclade_dataset_reference = "MN908947"
-    String nextclade_dataset_tag = "2022-09-27T12:00:00Z"
+    String nextclade_dataset_tag = "2022-12-14T12:00:00Z"
     String? nextclade_dataset_name
     String organism = "sars-cov-2"
   }

diff --git a/workflows/wf_theiacov_illumina_pe.wdl b/workflows/wf_theiacov_illumina_pe.wdl
@@ -25,7 +25,7 @@ workflow theiacov_illumina_pe {
     File read2_raw
     File? primer_bed
     String nextclade_dataset_reference = "MN908947"
-    String nextclade_dataset_tag = "2022-09-27T12:00:00Z"
+    String nextclade_dataset_tag = "2022-12-14T12:00:00Z"
     String? nextclade_dataset_name
     File? reference_gff
     File? reference_genome