[TheiaProk] update export_taxon_table and documentation (#814)

* Bump version

* update taxon tables

* more doc updates

* add |

* add input/output to theiaeuk too

Author: sage-wright

docs/workflows/genomic_characterization/theiacov.md

@@ -501,7 +501,7 @@ All TheiaCoV Workflows (not TheiaCoV_FASTA_Batch)
     | theiacov_fasta_batch | **nextclade_dataset_name** | String | Nextclade organism dataset name. Options: "nextstrain/sars-cov-2/wuhan-hu-1/orfs" However, if organism input is set correctly, this input will be automatically assigned the corresponding dataset name. | sars-cov-2 | Optional |
     | theiacov_fasta_batch | **nextclade_dataset_tag** | String | Nextclade dataset tag. Used for pulling up-to-date reference genomes and associated information specific to nextclade datasets (QC thresholds, organism-specific information like SARS-CoV-2 clade & lineage information, etc.) that is required for running the Nextclade tool.  | 2024-06-13--23-42-47Z | Optional |
     | theiacov_fasta_batch | **organism** | String | The organism that is being analyzed. Options: "sars-cov-2" | sars-cov-2 | Optional |
-    | theiacov_fasta_batch | **pangolin_docker** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/staphb/pangolin:4.3.1-pdata-1.27 | Optional |
+    | theiacov_fasta_batch | **pangolin_docker** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/staphb/pangolin:4.3.1-pdata-1.33 | Optional |
     | version_capture | **docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0" | Optional |
     | version_capture | **timezone** | String | Set the time zone to get an accurate date of analysis (uses UTC by default) |  | Optional |
 

docs/workflows/genomic_characterization/theiaeuk.md

@@ -4,7 +4,7 @@
 
 | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibliity** | **Workflow Level** |
 |---|---|---|---|---|
-| [Genomic Characterization](../../workflows_overview/workflows_type.md/#genomic-characterization) | [Mycotics](../../workflows_overview/workflows_kingdom.md/#mycotics) | PHB v3.0.0 | Yes | Sample-level |
+| [Genomic Characterization](../../workflows_overview/workflows_type.md/#genomic-characterization) | [Mycotics](../../workflows_overview/workflows_kingdom.md/#mycotics) | PHB v3.0.1 | Yes | Sample-level |
 
 ## TheiaEuk Workflows
 
@@ -48,8 +48,11 @@ All input reads are processed through "core tasks" in each workflow. The core ta
 | gambit | **disk_size** | Int | Amount of storage (in GB) to allocate to the task | 100 | Optional |
 | gambit | **docker** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/staphb/gambit:1.0.0 | Optional |
 | merlin_magic | **agrvate_docker_image** | String | Internal component, do not modify | "us-docker.pkg.dev/general-theiagen/biocontainers/agrvate:1.0.2--hdfd78af_0" | Do Not Modify, Optional |
-| merlin_magic | **run_amr_search** | Boolean | If set to true AMR_Search workflow will be run if species is part of supported taxon, see AMR_Search docs. | False | Optional |
 | merlin_magic | **assembly_only** | Boolean | Internal component, do not modify |  | Do Not Modify, Optional |
+| merlin_magic | **amr_search_cpu** | Int | Number of CPUs to allocate to the task | 2 | Optional |
+| merlin_magic | **amr_search_disk_size** | Int | Amount of storage (in GB) to allocate to the task | 50 | Optional |
+| merlin_magic | **amr_search_docker_image** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/theiagen/amrsearch:0.2.1 | Optional |
+| merlin_magic | **amr_search_memory** | Int | Amount of memory/RAM (in GB) to allocate to the task | 8 | Optional |
 | merlin_magic | **call_poppunk** | Boolean | Internal component, do not modify | TRUE | Do Not Modify, Optional |
 | merlin_magic | **call_shigeifinder_reads_input** | Boolean | Internal component, do not modify | FALSE | Do Not Modify, Optional |
 | merlin_magic | **emmtypingtool_docker_image** | String | Internal component, do not modify | us-docker.pkg.dev/general-theiagen/staphb/emmtypingtool:0.0.1 | Do Not Modify, Optional |
@@ -59,6 +62,7 @@ All input reads are processed through "core tasks" in each workflow. The core ta
 | merlin_magic | **pasty_docker_image** | String | Internal component, do not modify | us-docker.pkg.dev/general-theiagen/staphb/pasty:1.0.3 | Do Not Modify, Optional |
 | merlin_magic | **pasty_min_coverage** | Int | Internal component, do not modify | 95 | Do Not Modify, Optional |
 | merlin_magic | **pasty_min_percent_identity** | Int | Internal component, do not modify | 95 | Do Not Modify, Optional |
+| merlin_magic | **run_amr_search** | Boolean | If set to true AMR_Search workflow will be run if species is part of supported taxon, see AMR_Search docs. | False | Optional |
 | merlin_magic | **shigatyper_docker_image** | String | Internal component, do not modify | us-docker.pkg.dev/general-theiagen/staphb/shigatyper:2.0.5 | Do Not Modify, Optional |
 | merlin_magic | **shigeifinder_docker_image** | String | Internal component, do not modify | us-docker.pkg.dev/general-theiagen/staphb/shigeifinder:1.3.5 | Do Not Modify, Optional |
 | merlin_magic | **snippy_query_gene** | String | Internal component, do not modify |  | Do Not Modify, Optional |
@@ -602,6 +606,11 @@ All input reads are processed through "core tasks" in the TheiaEuk workflows. Th
 |---|---|---|
 | assembly_fasta | File | _De novo_ genome assembly in FASTA format |
 | assembly_length | Int | Length of assembly (total number of nucleotides) as determined by QUAST |
+| amr_results_csv | File | CSV formatted AMR profile |
+| amr_results_pdf | File | PDF formatted AMR profile |
+| amr_search_results | File | JSON formatted AMR profile including BLAST results |
+| amr_search_docker | String | Docker image used to run AMR_Search |
+| amr_search_version | String | Version of AMR_Search libraries used |
 | bbduk_docker| String | BBDuk docker image used |
 | busco_database | String | BUSCO database used |
 | busco_docker | String | BUSCO docker image used |

docs/workflows/genomic_characterization/theiaprok.md

@@ -108,7 +108,7 @@ All input reads are processed through "[core tasks](#core-tasks-performed-for-al
 | amrfinderplus_task | **cpu** | Int | Number of CPUs to allocate to the task | 2 | Optional | FASTA, ONT, PE, SE |
 | amrfinderplus_task | **detailed_drug_class** | Boolean | If set to true, amrfinderplus_amr_classes and amrfinderplus_amr_subclasses outputs will be created | FALSE | Optional | FASTA, ONT, PE, SE |
 | amrfinderplus_task | **disk_size** | Boolean | Amount of storage (in GB) to allocate to the AMRFinderPlus task | 50 | Optional | FASTA, ONT, PE, SE |
-| amrfinderplus_task | **docker** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/staphb/ncbi-amrfinderplus:3.12.8-2024-07-22.1 | Optional | FASTA, ONT, PE, SE |
+| amrfinderplus_task | **docker** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/staphb/ncbi-amrfinderplus:4.0.19-2024-12-18.1 | Optional | FASTA, ONT, PE, SE |
 | amrfinderplus_task | **hide_point_mutations** | Boolean | If set to true, point mutations are not reported | FALSE | Optional | FASTA, ONT, PE, SE |
 | amrfinderplus_task | **memory** | Int | Amount of memory/RAM (in GB) to allocate to the task | 8 | Optional | FASTA, ONT, PE, SE |
 | amrfinderplus_task | **min_percent_coverage** | Float | Minimum proportion of reference gene covered for a BLAST-based hit (Methods BLAST or PARTIAL)." Attribute should be a float ranging from 0-1, such as 0.6 (equal to 60% coverage) | 0.5 | Optional| FASTA, ONT, PE, SE |
@@ -232,7 +232,10 @@ All input reads are processed through "[core tasks](#core-tasks-performed-for-al
 | merlin_magic | **abricate_vibrio_min_percent_identity** | Int | Minimum DNA percent identity | 80 | Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **agrvate_agr_typing_only** | Boolean | Set to true to skip agr operon extraction and frameshift detection | False  | Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **agrvate_docker_image** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/biocontainers/agrvate:1.0.2--hdfd78af_0 | Optional | FASTA, ONT, PE, SE |
-| merlin_magic | **run_amr_search** | Boolean | If set to true AMR_Search workflow will be run if species is part of supported taxon, see AMR_Search docs. | False | Optional | FASTA, ONT, PE, SE |
+| merlin_magic | **amr_search_cpu** | Int | Number of CPUs to allocate to the task | 2 | Optional | FASTA, ONT, PE, SE |
+| merlin_magic | **amr_search_disk_size** | Int | Amount of storage (in GB) to allocate to the task | 50 | Optional | FASTA, ONT, PE, SE |
+| merlin_magic | **amr_search_docker_image** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/theiagen/amrsearch:0.2.1 | Optional | FASTA, ONT, PE, SE |
+| merlin_magic | **amr_search_memory** | Int | Amount of memory/RAM (in GB) to allocate to the task | 8 | Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **assembly_only** | Boolean | Internal component, do not modify |  | Do not modify, Optional | ONT, PE, SE |
 | merlin_magic | **call_poppunk** | Boolean | If "true", runs PopPUNK for GPSC cluster designation for S. pneumoniae | TRUE | Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **call_shigeifinder_reads_input** | Boolean | If set to "true", the ShigEiFinder task will run again but using read files as input instead of the assembly file. Input is shown but not used for TheiaProk_FASTA. | FALSE | Optional | FASTA, ONT, PE, SE |
@@ -310,6 +313,7 @@ All input reads are processed through "[core tasks](#core-tasks-performed-for-al
 | merlin_magic | **poppunk_gps_unword_clusters_csv** | File | Poppunk database file *Provide an empty or local file if running TheiaProk on the command-line | gs://theiagen-public-files-rp/terra/theiaprok-files/GPS_v6/GPS_v6_unword_clusters.csv | Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **read1** | File | Internal component, do not modify |  | Do not modify, Optional | FASTA |
 | merlin_magic | **read2** | File | Internal component, do not modify |  | Do not modify, Optional | FASTA, ONT, SE |
+| merlin_magic | **run_amr_search** | Boolean | If set to true AMR_Search workflow will be run if species is part of supported taxon, see AMR_Search docs. | False | Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **seqsero2_docker_image** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/staphb/seqsero2:1.2.1 | Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **seroba_docker_image** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/staphb/seroba:1.0.2 | Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **serotypefinder_docker_image** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/staphb/serotypefinder:2.0.1 | Optional | FASTA, ONT, PE, SE |
@@ -1827,6 +1831,11 @@ The TheiaProk workflows automatically activate taxa-specific sub-workflows after
 | agrvate_results | File | A gzipped tarball of all results | FASTA, ONT, PE, SE |
 | agrvate_summary | File | The summary file produced | FASTA, ONT, PE, SE |
 | agrvate_version | String | The version of AgrVATE used | FASTA, ONT, PE, SE |
+| amr_results_csv | File | CSV formatted AMR profile | FASTA, ONT, PE, SE |
+| amr_results_pdf | File | PDF formatted AMR profile |  FASTA, ONT, PE, SE |
+| amr_search_results | File | JSON formatted AMR profile including BLAST results | FASTA, ONT, PE, SE |
+| amr_search_docker | String | Docker image used to run AMR_Search | FASTA, ONT, PE, SE |
+| amr_search_version | String | Version of AMR_Search libraries used | FASTA, ONT, PE, SE |
 | amrfinderplus_all_report | File | Output TSV file from AMRFinderPlus (described <https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus#fields>) | FASTA, ONT, PE, SE |
 | amrfinderplus_amr_betalactam_betalactam_genes | String | Beta-lactam AMR genes identified by AMRFinderPlus that are known to confer resistance to beta-lactams  | FASTA, ONT, PE, SE |
 | amrfinderplus_amr_betalactam_carbapenem_genes | String | Beta-lactam AMR genes identified by AMRFinderPlus that are known to confer resistance to carbapenem  | FASTA, ONT, PE, SE |

docs/workflows/genomic_characterization/vadr_update.md

@@ -2,10 +2,9 @@
 
 ## Quick Facts
 
-
 | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** |
 |---|---|---|---|---|
-| [Genomic Characterization](../../workflows_overview/workflows_type.md/#genomic-characterization) | [Viral](../../workflows_overview/workflows_kingdom.md/#viral) | PHB v2.2.0 | Yes | Sample-level |
+| [Genomic Characterization](../../workflows_overview/workflows_type.md/#genomic-characterization) | [Viral](../../workflows_overview/workflows_kingdom.md/#viral) | PHB v3.0.1 | Yes | Sample-level |
 
 ## Vadr_Update_PHB
 

docs/workflows/standalone/amr_search.md

@@ -31,9 +31,9 @@ A limited number of species are currently supported and are listed below. NCBI c
 
 | **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** |
 |---|---|---|---|---|---|
-| amr_search_workflow | **amr_search_database** | String | NCBI taxon code of samples known taxonomy, see above supported species || Required |
+| amr_search_workflow | **amr_search_database** | String | NCBI taxon code of samples known taxonomy, see above supported species | | Required |
 | amr_search_workflow | **input_fasta** | File | A microbial assembly file || Required |
-| amr_search_workflow | **samplename** | String | Identifier user wants prefixed to output files || Required |
+| amr_search_workflow | **samplename** | String | Identifier user wants prefixed to output files | | Required |
 | amr_search | **cpu** | Integer | Number of CPUs to allocate to the task |2| Optional |
 | amr_search | **disk_size** | Integer | Amount of storage (in GB) to allocate to the task |50| Optional |
 | amr_search | **docker** | String | The docker container to use for the task |us-docker.pkg.dev/general-theiagen/theiagen/amrsearch:0.2.0| Optional |

docs/workflows_overview/workflows_alphabetically.md

@@ -54,7 +54,7 @@ title: Alphabetical Workflows
 | [**Transfer_Column_Content**](../workflows/data_export/transfer_column_content.md)| Transfer contents of a specified Terra data table column for many samples ("entities") to a GCP storage bucket location | Any taxa | Set-level | Yes | v1.3.0 | [Transfer_Column_Content_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Transfer_Column_Content_PHB:main?tab=info) |
 | [**Samples_to_Ref_Tree**](../workflows/phylogenetic_placement/usher.md)| Use UShER to rapidly and accurately place your samples on any existing phylogenetic tree | Monkeypox virus, SARS-CoV-2, Viral | Sample-level, Set-level | Yes | v2.1.0 | [Usher_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Usher_PHB:main?tab=info) |
 | [**Usher_PHB**](../workflows/genomic_characterization/vadr_update.md)| Update VADR assignments | HAV, Influenza, Monkeypox virus, RSV-A, RSV-B, SARS-CoV-2, Viral, WNV | Sample-level | Yes | v2.1.0 | [VADR_Update_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/VADR_Update_PHB:main?tab=info) |
-| [**VADR_Update**](../workflows/genomic_characterization/vadr_update.md)| Update VADR assignments | HAV, Influenza, Monkeypox virus, RSV-A, RSV-B, SARS-CoV-2, Viral, WNV | Sample-level | Yes | v2.2.0 | [VADR_Update_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/VADR_Update_PHB:main?tab=info) |
+| [**VADR_Update**](../workflows/genomic_characterization/vadr_update.md)| Update VADR assignments | HAV, Influenza, Monkeypox virus, RSV-A, RSV-B, SARS-CoV-2, Viral, WNV | Sample-level | Yes | v3.0.1 | [VADR_Update_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/VADR_Update_PHB:main?tab=info) |
 | [**Zip_Column_Content**](../workflows/data_export/zip_column_content.md)| Zip contents of a specified Terra data table column for many samples ("entities") | Any taxa | Set-level | Yes | v2.1.0 | [Zip_Column_Content_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Zip_Column_Content_PHB:main?tab=info) |
 
 </div>

docs/workflows_overview/workflows_kingdom.md

@@ -96,7 +96,7 @@ title: Workflows by Kingdom
 | [**Terra_2_NCBI**](../workflows/public_data_sharing/terra_2_ncbi.md)| Upload of sequence data to NCBI | Bacteria, Mycotics, Viral | Set-level | No | v3.0.0 | [Terra_2_NCBI_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Terra_2_NCBI_PHB:main?tab=info) |
 | [**TheiaCov Workflow Series**](../workflows/genomic_characterization/theiacov.md) | Viral genome assembly, QC and characterization from amplicon sequencing | HIV, Influenza, Monkeypox virus, RSV-A, RSV-B, SARS-CoV-2, Viral, WNV | Sample-level, Set-level | Some optional features incompatible, Yes | v3.0.1 | [TheiaCoV_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaCoV_Illumina_PE_PHB:main?tab=info), [TheiaCoV_Illumina_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaCoV_Illumina_SE_PHB:main?tab=info), [TheiaCoV_ONT_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaCoV_ONT_PHB:main?tab=info), [TheiaCoV_ClearLabs_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaCoV_ClearLabs_PHB:main?tab=info), [TheiaCoV_FASTA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaCoV_FASTA_PHB:main?tab=info), [TheiaCoV_FASTA_Batch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaCoV_FASTA_Batch_PHB:main?tab=info) |
 | [**Usher_PHB**](../workflows/phylogenetic_placement/usher.md)| Use UShER to rapidly and accurately place your samples on any existing phylogenetic tree | Monkeypox virus, SARS-CoV-2, Viral | Sample-level, Set-level | Yes | v2.1.0 | [Usher_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Usher_PHB:main?tab=info) |
-| [**VADR_Update**](../workflows/genomic_characterization/vadr_update.md)| Update VADR assignments | HAV, Influenza, Monkeypox virus, RSV-A, RSV-B, SARS-CoV-2, Viral, WNV | Sample-level | Yes | v2.2.0 | [VADR_Update_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/VADR_Update_PHB:main?tab=info) |
+| [**VADR_Update**](../workflows/genomic_characterization/vadr_update.md)| Update VADR assignments | HAV, Influenza, Monkeypox virus, RSV-A, RSV-B, SARS-CoV-2, Viral, WNV | Sample-level | Yes | v3.0.1 | [VADR_Update_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/VADR_Update_PHB:main?tab=info) |
 
 </div>