[Documentation] update dataset tags (#681)

* Update nextclade dataset tags and pangolin docker version for TheiaCoV workflows

* Add searchable table for organism-specific parameters in TheiaCoV documentation

* Enhance TheiaCoV documentation with searchable tables for organism-specific parameters

docs/workflows/genomic_characterization/theiacov.md

@@ -481,34 +481,44 @@ The `organism_parameters` sub-workflow is the first step in all TheiaCoV workflo
     The following tables include the relevant organism-specific parameters; **all of these default values can be overwritten by providing a value for the "Overwrite Variable Name" field**.
 
     ??? toggle "SARS-CoV-2 Defaults"
+        <div class="searchable-table" markdown="block">
+
         | **Overwrite Variable Name** | **Organism** | **Default Value** |
         |---|---|---|
         | gene_locations_bed_file | sars-cov-2 | `"gs://theiagen-public-files-rp/terra/sars-cov-2-files/sc2_gene_locations.bed"` |
         | genome_length_input | sars-cov-2 | `29903` |
         | nextclade_dataset_name_input | sars-cov-2 | `"nextstrain/sars-cov-2/wuhan-hu-1/orfs"` |
-        | nextclade_dataset_tag_input | sars-cov-2 | `"2024-07-17--12-57-03Z"` |
-        | pangolin_docker_image | sars-cov-2 | `"us-docker.pkg.dev/general-theiagen/staphb/pangolin:4.3.1-pdata-1.29 "`|
+        | nextclade_dataset_tag_input | sars-cov-2 | `"2024-11-19--14-18-53Z"` |
+        | pangolin_docker_image | sars-cov-2 | `"us-docker.pkg.dev/general-theiagen/staphb/pangolin:4.3.1-pdata-1.31 "`|
         | reference_genome | sars-cov-2 | `"gs://theiagen-public-files-rp/terra/augur-sars-cov-2-references/MN908947.fasta"` |
         | vadr_max_length | sars-cov-2 | `30000` |
         | vadr_mem | sars-cov-2 | `8` |
         | vadr_options | sars-cov-2 | `"--noseqnamemax --glsearch -s -r --nomisc --mkey sarscov2 --lowsim5seq 6 --lowsim3seq 6 --alt_fail lowscore,insertnn,deletinn --out_allfasta"` |
 
+        </div>
+
     ??? toggle "Mpox Defaults"
+        <div class="searchable-table" markdown="block">
+
         | **Overwrite Variable Name** | **Organism** | **Default Value** |
         |---|---|---|
         | gene_locations_bed_file | MPXV | `"gs://theiagen-public-files/terra/mpxv-files/mpox_gene_locations.bed"` |
         | genome_length_input | MPXV | `197200` |
         | kraken_target_organism_input | MPXV | `"Monkeypox virus"` |
         | nextclade_dataset_name_input | MPXV | `"nextstrain/mpox/lineage-b.1"` |
-        | nextclade_dataset_tag_input | MPXV | `"2024-04-19--07-50-39Z"` |
+        | nextclade_dataset_tag_input | MPXV | `"2024-11-19--14-18-53Z"` |
         | primer_bed_file | MPXV | `"gs://theiagen-public-files/terra/mpxv-files/MPXV.primer.bed"` |
         | reference_genome | MPXV | `"gs://theiagen-public-files/terra/mpxv-files/MPXV.MT903345.reference.fasta"` |
         | reference_gff_file | MPXV | `"gs://theiagen-public-files/terra/mpxv-files/Mpox-MT903345.1.reference.gff3"` |
         | vadr_max_length | MPXV | `210000` |
         | vadr_mem | MPXV | `8` |
         | vadr_options | MPXV | `"--glsearch -s -r --nomisc --mkey mpxv --r_lowsimok --r_lowsimxd 100 --r_lowsimxl 2000 --alt_pass discontn,dupregin --out_allfasta --minimap2 --s_overhang 150"` |
+        
+        </div>
 
     ??? toggle "WNV Defaults"
+        <div class="searchable-table" markdown="block">
+
         | **Overwrite Variable Name** | **Organism** | **Default Value** | **Notes** |
         |---|---|---|---|
         | genome_length_input | WNV | `11000` | |
@@ -521,7 +531,11 @@ The `organism_parameters` sub-workflow is the first step in all TheiaCoV workflo
         | vadr_mem | WNV | `8` |  |
         | vadr_options | WNV | `"--mkey flavi --mdir /opt/vadr/vadr-models-flavi/ --nomisc --noprotid --out_allfasta"` |  |
 
+        </div>
+
     ??? toggle "Flu Defaults"
+        <div class="searchable-table" markdown="block">
+
         | **Overwrite Variable Name** | **Organism** | **Flu Segment** | **Flu Subtype** | **Default Value** | **Notes** |
         |---|---|---|---|---|---|
         | flu_segment | flu | all | all | N/A | TheiaCoV will attempt to automatically assign a flu segment  |
@@ -531,13 +545,13 @@ The `organism_parameters` sub-workflow is the first step in all TheiaCoV workflo
         | vadr_mem | flu | all | all | `8` |  |
         | vadr_options | flu | all | all | `"--atgonly --xnocomp --nomisc --alt_fail extrant5,extrant3 --mkey flu"` |  |
         | nextclade_dataset_name_input | flu | ha | h1n1 | `"nextstrain/flu/h1n1pdm/ha/MW626062"` |  |
-        | nextclade_dataset_tag_input | flu | ha | h1n1 | `"2024-07-03--08-29-55Z"` |  |
+        | nextclade_dataset_tag_input | flu | ha | h1n1 | `"2024-11-27--02-51-00Z"` |  |
         | reference_genome | flu | ha | h1n1 | `"gs://theiagen-public-files-rp/terra/flu-references/reference_h1n1pdm_ha.fasta"` |  |
         | nextclade_dataset_name_input | flu | ha | h3n2 | `"nextstrain/flu/h3n2/ha/EPI1857216"` |  |
-        | nextclade_dataset_tag_input | flu | ha | h3n2 | `"2024-08-08--05-08-21Z"` |  |
+        | nextclade_dataset_tag_input | flu | ha | h3n2 | `"2024-11-27--02-51-00Z"` |  |
         | reference_genome | flu | ha | h3n2 | `"gs://theiagen-public-files-rp/terra/flu-references/reference_h3n2_ha.fasta"` |  |
         | nextclade_dataset_name_input | flu | ha | victoria | `"nextstrain/flu/vic/ha/KX058884"` |  |
-        | nextclade_dataset_tag_input | flu | ha | victoria | `"2024-07-03--08-29-55Z"` |  |
+        | nextclade_dataset_tag_input | flu | ha | victoria | `"2024-11-05--09-19-52Z"` |  |
         | reference_genome | flu | ha | victoria | `"gs://theiagen-public-files-rp/terra/flu-references/reference_vic_ha.fasta"` |  |
         | nextclade_dataset_name_input | flu | ha | yamagata | `"nextstrain/flu/yam/ha/JN993010"` |  |
         | nextclade_dataset_tag_input | flu | ha | yamagata | `"2024-01-30--16-34-55Z"` |  |
@@ -546,43 +560,55 @@ The `organism_parameters` sub-workflow is the first step in all TheiaCoV workflo
         | nextclade_dataset_tag_input | flu | ha | h5n1 | `"2024-05-08--11-39-52Z"` |  |
         | reference_genome | flu | ha | h5n1 | `"gs://theiagen-public-files-rp/terra/flu-references/reference_h5n1_ha.fasta"` |  |
         | nextclade_dataset_name_input | flu | na | h1n1 | `"nextstrain/flu/h1n1pdm/na/MW626056"` |  |
-        | nextclade_dataset_tag_input | flu | na | h1n1 | `"2024-07-03--08-29-55Z"` |  |
+        | nextclade_dataset_tag_input | flu | na | h1n1 | `"2024-11-05--09-19-52Z"` |  |
         | reference_genome | flu | na | h1n1 | `"gs://theiagen-public-files-rp/terra/flu-references/reference_h1n1pdm_na.fasta"` |  |
         | nextclade_dataset_name_input | flu | na | h3n2 | `"nextstrain/flu/h3n2/na/EPI1857215"` |  |
-        | nextclade_dataset_tag_input | flu | na | h3n2 | `"2024-04-19--07-50-39Z"` |  |
+        | nextclade_dataset_tag_input | flu | na | h3n2 | `"2024-11-05--09-19-52Z"` |  |
         | reference_genome | flu | na | h3n2 | `"gs://theiagen-public-files-rp/terra/flu-references/reference_h3n2_na.fasta"` |  |
         | nextclade_dataset_name_input | flu | na | victoria | `"nextstrain/flu/vic/na/CY073894"` |  |
-        | nextclade_dataset_tag_input | flu | na | victoria | `"2024-04-19--07-50-39Z"` |  |
+        | nextclade_dataset_tag_input | flu | na | victoria | `"2024-11-05--09-19-52Z"` |  |
         | reference_genome | flu | na | victoria | `"gs://theiagen-public-files-rp/terra/flu-references/reference_vic_na.fasta"` |  |
         | nextclade_dataset_name_input | flu | na | yamagata | `"NA"` |  |
         | nextclade_dataset_tag_input | flu | na | yamagata | `"NA"` |  |
         | reference_genome | flu | na | yamagata | `"gs://theiagen-public-files-rp/terra/flu-references/reference_yam_na.fasta"` |  |
 
+        </div>
+
     ??? toggle "RSV-A Defaults"
+        <div class="searchable-table" markdown="block">
+
         | **Overwrite Variable Name** | **Organism** | **Default Value** |
         |---|---|---|
         | genome_length_input | rsv_a | 16000 |
         | kraken_target_organism | rsv_a | Respiratory syncytial virus |
         | nextclade_dataset_name_input | rsv_a | nextstrain/rsv/a/EPI_ISL_412866 |
-        | nextclade_dataset_tag_input | rsv_a | 2024-08-01--22-31-31Z |
+        | nextclade_dataset_tag_input | rsv_a | "2024-11-27--02-51-00Z" |
         | reference_genome | rsv_a | gs://theiagen-public-files-rp/terra/rsv_references/reference_rsv_a.fasta |
         | vadr_max_length | rsv_a | 15500 |
         | vadr_mem | rsv_a | 32 |
         | vadr_options | rsv_a | -r --mkey rsv --xnocomp |
 
+        </div>
+
     ??? toggle "RSV-B Defaults"
+        <div class="searchable-table" markdown="block">
+
         | **Overwrite Variable Name** | **Organism** | **Default Value** |
         |---|---|---|
         | genome_length_input | rsv_b | 16000 |
         | kraken_target_organism | rsv_b |  "Human orthopneumovirus" |
         | nextclade_dataset_name_input | rsv_b | nextstrain/rsv/b/EPI_ISL_1653999 |
-        | nextclade_dataset_tag_input | rsv_b | "2024-08-01--22-31-31Z" |
+        | nextclade_dataset_tag_input | rsv_b | "2024-11-27--02-51-00Z" |
         | reference_genome | rsv_b | gs://theiagen-public-files-rp/terra/rsv_references/reference_rsv_b.fasta |
         | vadr_max_length | rsv_b | 15500 |
         | vadr_mem | rsv_b | 32 |
         | vadr_options | rsv_b | -r --mkey rsv --xnocomp |
 
+        </div>
+
     ??? toggle "HIV Defaults"
+        <div class="searchable-table" markdown="block">
+
         | **Overwrite Variable Name** | **Organism** | **Default Value** | **Notes** |
         |---|---|---|---|
         | kraken_target_organism_input | HIV | Human immunodeficiency virus 1 |  |
@@ -595,6 +621,8 @@ The `organism_parameters` sub-workflow is the first step in all TheiaCoV workflo
         | reference_genome | HIV-v2 | gs://theiagen-public-files/terra/hivgc-files/AY228557.1.headerchanged.fasta | This version of HIV originates from Southern Africa |
         | reference_gff_file | HIV-v2 | gs://theiagen-public-files/terra/hivgc-files/AY228557.1.gff3 | This version of HIV originates from Southern Africa |
 
+        </div>
+
 ### Workflow Tasks
 
 All input reads are processed through "core tasks" in the TheiaCoV Illumina, ONT, and ClearLabs workflows. These undertake read trimming and assembly appropriate to the input data type. TheiaCoV workflows subsequently launch default genome characterization modules for quality assessment, and additional taxa-specific characterization steps. When setting up the workflow, users may choose to use "optional tasks" as additions or alternatives to tasks run in the workflow by default.