diff --git a/.dockstore.yml b/.dockstore.yml
index 146638eb7..aa87c3835 100644
--- a/.dockstore.yml
+++ b/.dockstore.yml
@@ -287,4 +287,9 @@ workflows:
    subclass: WDL
    primaryDescriptorPath: /workflows/phylogenetics/wf_snippy_streamline_fasta.wdl
    testParameterFiles:
-    - /tests/inputs/empty.json
\ No newline at end of file
+    - /tests/inputs/empty.json
+ - name: Concatenate_Illumina_Lanes_PHB
+   subclass: WDL
+   primaryDescriptorPath: /workflows/utilities/file_handling/wf_concatenate_illumina_lanes.wdl
+   testParameterFiles:
+     - /tests/inputs/empty.json
\ No newline at end of file
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 3aebe21d9..96f294e54 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -45,7 +45,8 @@ This PR uses an element that could cause duplicate runs to have different result
 - [ ] The workflow/task has been tested and results, including file contents, are as anticipated
 - [ ] The CI/CD has been adjusted and tests are passing (Theiagen developers)
 - [ ] Code changes follow the [style guide](https://theiagen.notion.site/Style-Guide-WDL-Workflow-Development-51b66a47dde54c798f35d673fff80249)
-- [ ] Documentation and/or workflow diagrams have been updated if applicable (Theiagen developers only)
+- [ ] Documentation and/or workflow diagrams have been updated if applicable
+  - [ ] You have updated the latest version for any affected worklows in the respective workflow documentation page and for every entry in the three `workflows_overview` tables.
 
 ## 🎯 Reviewer Checklist
 <!--  Indicate NA when not applicable  -->
diff --git a/docs/workflows/genomic_characterization/theiacov.md b/docs/workflows/genomic_characterization/theiacov.md
index 3e2ad8956..480bfbf04 100644
--- a/docs/workflows/genomic_characterization/theiacov.md
+++ b/docs/workflows/genomic_characterization/theiacov.md
@@ -4,7 +4,7 @@
 
 | **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, some optional features incompatible | Sample-level |
+| [Genomic Characterization](../../workflows_overview/workflows_type.md/#genomic-characterization) | [Viral](../../workflows_overview/workflows_kingdom.md/#viral) | PHB v2.3.0 | Yes, some optional features incompatible | Sample-level |
 
 ## TheiaCoV Workflows
 
diff --git a/docs/workflows/genomic_characterization/theiaeuk.md b/docs/workflows/genomic_characterization/theiaeuk.md
index cc9cba9c1..2bfc2e6cf 100644
--- a/docs/workflows/genomic_characterization/theiaeuk.md
+++ b/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 v2.2.0 | Yes | Sample-level |
+| [Genomic Characterization](../../workflows_overview/workflows_type.md/#genomic-characterization) | [Mycotics](../../workflows_overview/workflows_kingdom.md/#mycotics) | PHB v2.3.0 | Yes | Sample-level |
 
 ## TheiaEuk Workflows
 
diff --git a/docs/workflows/genomic_characterization/theiameta.md b/docs/workflows/genomic_characterization/theiameta.md
index d6b55e80a..fad3c359a 100644
--- a/docs/workflows/genomic_characterization/theiameta.md
+++ b/docs/workflows/genomic_characterization/theiameta.md
@@ -4,7 +4,7 @@
 
 | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** |
 |---|---|---|---|---|
-| [Genomic Characterization](../../workflows_overview/workflows_type.md/#genomic-characterization) | [Any Taxa](../../workflows_overview/workflows_kingdom.md/#any-taxa) | PHB v2.2.0 | Yes | Sample-level |
+| [Genomic Characterization](../../workflows_overview/workflows_type.md/#genomic-characterization) | [Any Taxa](../../workflows_overview/workflows_kingdom.md/#any-taxa) | PHB v2.3.0 | Yes | Sample-level |
 
 ## TheiaMeta Workflows
 
diff --git a/docs/workflows/genomic_characterization/theiaprok.md b/docs/workflows/genomic_characterization/theiaprok.md
index 8808caab2..d3dbb55b0 100644
--- a/docs/workflows/genomic_characterization/theiaprok.md
+++ b/docs/workflows/genomic_characterization/theiaprok.md
@@ -4,7 +4,7 @@
 
 | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** |
 |---|---|---|---|---|
-| [Genomic Characterization](../../workflows_overview/workflows_type.md/#genomic-characterization) | [Bacteria](../../workflows_overview/workflows_kingdom.md/#bacteria) | PHB v2.2.0 | Yes, some optional features incompatible | Sample-level |
+| [Genomic Characterization](../../workflows_overview/workflows_type.md/#genomic-characterization) | [Bacteria](../../workflows_overview/workflows_kingdom.md/#bacteria) | PHB v2.3.0 | Yes, some optional features incompatible | Sample-level |
 
 ## TheiaProk Workflows
 
@@ -78,6 +78,12 @@ All input reads are processed through "[core tasks](#core-tasks-performed-for-al
 | *workflow name | **originating_lab** | String | Will be used in the "originating_lab" column in any taxon-specific tables created in the Export Taxon Tables task |  | Optional | FASTA, ONT, PE, SE |
 | *workflow name | **perform_characterization** | Boolean | Set to "false" if you want to only generate an assembly and relevant QC metrics and skip all characterization tasks | TRUE | Optional | FASTA, ONT, PE, SE |
 | *workflow name | **qc_check_table** | File | TSV value with taxons for rows and QC values for columns; internal cells represent user-determined QC thresholds; if provided, turns on the QC Check task.<br>Click on the variable name for an example QC Check table |  | Optional | FASTA, ONT, PE, SE |
+| *workflow name | **read1_lane2** | File | If provided, the Concatenate_Illumina_Lanes subworkflow will concatenate all files from the same lane before doing any subsequent analysis |  | Optional | PE, SE |
+| *workflow name | **read1_lane3** | File | If provided, the Concatenate_Illumina_Lanes subworkflow will concatenate all files from the same lane before doing any subsequent analysis |  | Optional | PE, SE |
+| *workflow name | **read1_lane4** | File | If provided, the Concatenate_Illumina_Lanes subworkflow will concatenate all files from the same lane before doing any subsequent analysis |  | Optional | PE, SE |
+| *workflow name | **read2_lane2** | File | If provided, the Concatenate_Illumina_Lanes subworkflow will concatenate all files from the same lane before doing any subsequent analysis |  | Optional | PE, SE |
+| *workflow name | **read2_lane3** | File | If provided, the Concatenate_Illumina_Lanes subworkflow will concatenate all files from the same lane before doing any subsequent analysis |  | Optional | PE, SE |
+| *workflow name | **read2_lane4** | File | If provided, the Concatenate_Illumina_Lanes subworkflow will concatenate all files from the same lane before doing any subsequent analysis |  | Optional | PE, SE | 
 | *workflow name | **run_id** | String | Will be used in the "run_id" column in any taxon-specific tables created in the Export Taxon Tables task |  | Optional | FASTA, ONT, PE, SE |
 | *workflow name | **seq_method** | String | Will be used in the "seq_id" column in any taxon-specific tables created in the Export Taxon Tables task |  | Optional | FASTA, ONT, PE, SE |
 | *workflow name | **skip_mash** | Boolean | If true, skips estimation of genome size and coverage in read screening steps. As a result, providing true also prevents screening using these parameters. | TRUE | Optional | ONT, SE |
@@ -301,6 +307,7 @@ All input reads are processed through "[core tasks](#core-tasks-performed-for-al
 | 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 |
 | merlin_magic | **call_stxtyper** | Boolean | If set to "true", the StxTyper task will run on all samples regardless of the `gambit_predicted_taxon` output. Useful if you suspect a non-E.coli or non-Shigella sample contains stx genes. | FALSE | Optional | FASTA, ONT, PE, SE |
+| merlin_magic | **call_tbp_parser** | Boolean | If set to "true", activates the tbp_parser module and results in more outputs, including tbp_parser_looker_report_csv, tbp_parser_laboratorian_report_csv,  tbp_parser_lims_report_csv, tbp_parser_coverage_report, and tbp_parser_genome_percent_coverage | FALSE | Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **cauris_cladetyper_docker_image** | String | Internal component, do not modify |  | Do not modify, Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **cladetyper_kmer_size** | Int | Internal component, do not modify |  | Do not modify, Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **cladetyper_ref_clade1** | File | *Provide an empty file if running TheiaProk on the command-line |  | Do not modify, Optional | FASTA, ONT, PE, SE |
@@ -407,27 +414,33 @@ All input reads are processed through "[core tasks](#core-tasks-performed-for-al
 | merlin_magic | **stxtyper_enable_debug** | Boolean | When enabled, additional messages are printed and files in `$TMPDIR` are not removed after running | FALSE | Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **stxtyper_memory** | Int | Amount of memory (in GB) to allocate to the task | 4 | Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **staphopia_sccmec_docker_image** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/biocontainers/staphopia-sccmec:1.0.0--hdfd78af_0 | Optional | FASTA, ONT, PE, SE |
+| merlin_magic | **tbp_parser_add_cs_lims** | Boolean | Set to true add cycloserine results to the LIMS report | FALSE | Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **tbp_parser_coverage_regions_bed** | File | A bed file that lists the regions to be considered for QC |  | Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **tbp_parser_coverage_threshold** | Int | The minimum coverage for a region to pass QC in tbp_parser | 100 | Optional | FASTA, ONT, PE, SE |
-| merlin_magic | **tbp_parser_debug** | Boolean | Activate the debug mode on tbp_parser; increases logging outputs | FALSE | Optional | FASTA, ONT, PE, SE |
-| merlin_magic | **tbp_parser_docker_image** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:1.6.0 | Optional | FASTA, ONT, PE, SE |
-| merlin_magic | **tbp_parser_docker_image** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:1.4.0 | Optional | FASTA, ONT, PE, SE |
+| merlin_magic | **tbp_parser_debug** | Boolean | Activate the debug mode on tbp_parser; increases logging outputs | TRUE | Optional | FASTA, ONT, PE, SE |
+| merlin_magic | **tbp_parser_docker_image** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:2.1.1 | Optional | FASTA, ONT, PE, SE |
+| merlin_magic | **tbp_parser_etha237_frequency** | Float | Minimum frequency for a mutation in ethA at protein position 237 to pass QC in tbp-parser | 0.1 | Optional | FASTA, ONT, PE, SE |
+| merlin_magic | **tbp_parser_expert_rule_regions_bed** | File | A file that contains the regions where R mutations and expert rules are applied |  | Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **tbp_parser_min_depth** | Int | Minimum depth for a variant to pass QC in tbp_parser | 10 | Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **tbp_parser_min_frequency** | Int | The minimum frequency for a mutation to pass QC | 0.1 | Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **tbp_parser_min_read_support** | Int | The minimum read support for a mutation to pass QC | 10 | Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **tbp_parser_operator** | String | Fills the "operator" field in the tbp_parser output files | Operator not provided | Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **tbp_parser_output_seq_method_type** | String | Fills out the "seq_method" field in the tbp_parser output files | Sequencing method not provided | Optional | FASTA, ONT, PE, SE |
-| merlin_magic | **tbprofiler_additional_outputs** | Boolean | If set to "true", activates the tbp_parser module and results in more outputs, including tbp_parser_looker_report_csv, tbp_parser_laboratorian_report_csv,  tbp_parser_lims_report_csv, tbp_parser_coverage_report, and tbp_parser_genome_percent_coverage | FALSE | Optional | FASTA, ONT, PE, SE |
-| merlin_magic | **tbprofiler_cov_frac_threshold** | Int | A cutoff used to calculate the fraction of the region covered by ≤ this value | 1 | Optional | FASTA, ONT, PE, SE |
+| merlin_magic | **tbp_parser_rpob449_frequency** | Float | Minimum frequency for a mutation at protein position 449 to pass QC in tbp-parser | 0.1 | Optional | FASTA, ONT, PE, SE |
+| merlin_magic | **tbp_parser_rrl_frequency** | Float | Minimum frequency for a mutation in rrl to pass QC in tbp-parser | 0.1 | Optional | FASTA, ONT, PE, SE |
+| merlin_magic | **tbp_parser_rrl_read_support** | Int | Minimum read support for a mutation in rrl to pass QC in tbp-parser | 10 | Optional | FASTA, ONT, PE, SE |
+| merlin_magic | **tbp_parser_rrs_frequency** | Float | Minimum frequency for a mutation in rrs to pass QC in tbp-parser | 0.1 | Optional | FASTA, ONT, PE, SE |
+| merlin_magic | **tbp_parser_rrs_read_support** | Int | Minimum read support for a mutation in rrs to pass QC in tbp-parser | 10 | Optional | FASTA, ONT, PE, SE |
+| merlin_magic | **tbp_parser_tngs_data** | Boolean | Set to true to enable tNGS-specific parameters and runs in tbp-parser | FALSE | Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **tbprofiler_custom_db** | File | TBProfiler uses by default the TBDB database; if you have a custom database you wish to use, you must provide a custom database in this field and set tbprofiler_run_custom_db to true |  | Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **tbprofiler_docker_image** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/staphb/tbprofiler:4.4.2 | Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **tbprofiler_mapper** | String | The mapping tool used in TBProfiler to align the reads to the reference genome; see TBProfiler’s original documentation for available options. | bwa | Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **tbprofiler_min_af** | Float | The minimum allele frequency to call a variant | 0.1 | Optional | FASTA, ONT, PE, SE |
-| merlin_magic | **tbprofiler_min_af_pred** | Float | The minimum allele frequency to use a variant for resistance prediction | 0.1 | Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **tbprofiler_min_depth** | Int | The minimum depth for a variant to be called. | 10 | Optional | FASTA, ONT, PE, SE |
+| merlin_magic | **tbprofiler_run_cdph_db** | Boolean | TBProfiler uses by default the TBDB database; set this value to "true" to use the WHO v2 database with customizations for CDPH | FALSE | Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **tbprofiler_run_custom_db** | Boolean | TBProfiler uses by default the TBDB database; if you have a custom database you wish to use, you must set this value to true and provide a custom database in the tbprofiler_custom_db field | FALSE | Optional | FASTA, ONT, PE, SE |
-| merlin_magic | **tbprofiler_variant_caller** | String | Select a different variant caller for TBProfiler to use by writing it in this block; see TBProfiler’s original documentation for available options. | freebayes | Optional | FASTA, ONT, PE, SE |
-| merlin_magic | **tbprofiler_variant_calling_params** | String | Enter additional variant calling parameters in this free text input to customize how the variant caller works in TBProfiler | None | Optional | FASTA, ONT, PE, SE |
+| merlin_magic | **tbprofiler_variant_caller** | String | Select a different variant caller for TBProfiler to use by writing it in this block; see TBProfiler’s original documentation for available options. | GATK | Optional | FASTA, ONT, PE, SE |
+| merlin_magic | **tbprofiler_variant_calling_params** | String | Enter additional variant calling parameters in this free text input to customize how the variant caller works in TBProfiler | | Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **theiaeuk** | Boolean | Internal component, do not modify |  | Do not modify, Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **virulencefinder_coverage_threshold** | Float | The threshold for minimum coverage |  | Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **virulencefinder_database** | String | The specific database to use | virulence_ecoli | Optional | FASTA, ONT, PE, SE |
@@ -594,6 +607,17 @@ All input reads are processed through "[core tasks](#core-tasks-performed-for-al
         | --- | --- |
         | Task | [task_versioning.wdl](https://github.com/theiagen/public_health_bioinformatics/blob/main/tasks/task_versioning.wdl) |
 
+??? task "`concatenate_illumina_lanes`: Concatenate Multi-Lane Illumina FASTQs ==_for Illumina only_=="
+
+    The `concatenate_illumina_lanes` task concatenates Illumina FASTQ files from multiple lanes into a single file. This task only runs if the `read1_lane2` input file has been provided. All read1 lanes are concatenated together and are used in subsequent tasks, as are the read2 lanes. These concatenated files are also provided as output.
+
+    !!! techdetails "Concatenate Illumina Lanes Technical Details"
+        The `concatenate_illumina_lanes` task is run before any downstream steps take place.
+        
+        |  | Links |
+        | --- | --- |
+        | Task | [wf_concatenate_illumina_lanes.wdl](https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/file_handling/wf_concatenate_illumina_lanes.wdl)
+
 ??? task "`screen`: Total Raw Read Quantification and Genome Size Estimation"
 
     The [`screen`](https://github.com/theiagen/public_health_bioinformatics/blob/main/tasks/quality_control/comparisons/task_screen.wdl) task ensures the quantity of sequence data is sufficient to undertake genomic analysis. It uses [`fastq-scan`](https://github.com/rpetit3/fastq-scan) and bash commands for quantification of reads and base pairs, and [mash](https://mash.readthedocs.io/en/latest/index.html) sketching to estimate the genome size and its coverage. At each step, the results are assessed relative to pass/fail criteria and thresholds that may be defined by optional user inputs. Samples that do not meet these criteria will not be processed further by the workflow:
@@ -2022,7 +2046,7 @@ The TheiaProk workflows automatically activate taxa-specific sub-workflows after
 | tbp_parser_version | String | Optional output. The version of tbp-parser | ONT, PE |
 | tbprofiler_dr_type | String | Drug resistance type predicted by TB-Profiler (sensitive, Pre-MDR, MDR, Pre-XDR, XDR) | ONT, PE, SE |
 | tbprofiler_main_lineage | String | Lineage(s) predicted by TBProfiler | ONT, PE, SE |
-| tbprofiler_median_coverage | Int | The median coverage of the H37Rv TB reference genome | ONT, PE |
+| tbprofiler_median_depth | Int | The median depth of the H37Rv TB reference genome covered by the sample | ONT, PE |
 | tbprofiler_output_bai | File | Index BAM file generated by mapping sequencing reads to reference genome by TBProfiler | ONT, PE, SE |
 | tbprofiler_output_bam | File | BAM alignment file produced by TBProfiler | ONT, PE, SE |
 | tbprofiler_output_file | File | CSV report from TBProfiler | ONT, PE, SE |
diff --git a/docs/workflows/genomic_characterization/vadr_update.md b/docs/workflows/genomic_characterization/vadr_update.md
index ceaa45fa8..b3d706d72 100644
--- a/docs/workflows/genomic_characterization/vadr_update.md
+++ b/docs/workflows/genomic_characterization/vadr_update.md
@@ -5,7 +5,7 @@
 
 | **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 v1.2.1 | Yes | Sample-level |
+| [Genomic Characterization](../../workflows_overview/workflows_type.md/#genomic-characterization) | [Viral](../../workflows_overview/workflows_kingdom.md/#viral) | PHB v2.2.0 | Yes | Sample-level |
 
 ## Vadr_Update_PHB
 
diff --git a/docs/workflows/phylogenetic_construction/augur.md b/docs/workflows/phylogenetic_construction/augur.md
index c9d144997..9e5f67637 100644
--- a/docs/workflows/phylogenetic_construction/augur.md
+++ b/docs/workflows/phylogenetic_construction/augur.md
@@ -4,7 +4,7 @@
 
 | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** |
 |---|---|---|---|---|
-| [Phylogenetic Construction](../../workflows_overview/workflows_type.md/#phylogenetic-construction) | [Viral](../../workflows_overview/workflows_kingdom.md/#viral) | PHB v2.1.0 | Yes | Sample-level, Set-level |
+| [Phylogenetic Construction](../../workflows_overview/workflows_type.md/#phylogenetic-construction) | [Viral](../../workflows_overview/workflows_kingdom.md/#viral) | PHB v2.3.0 | Yes | Sample-level, Set-level |
 
 ## Augur Workflows
 
diff --git a/docs/workflows/phylogenetic_construction/snippy_streamline.md b/docs/workflows/phylogenetic_construction/snippy_streamline.md
index aa04198b3..facc3e1c4 100644
--- a/docs/workflows/phylogenetic_construction/snippy_streamline.md
+++ b/docs/workflows/phylogenetic_construction/snippy_streamline.md
@@ -4,7 +4,7 @@
 
 | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** |
 |---|---|---|---|---|
-| [Phylogenetic Construction](../../workflows_overview/workflows_type.md/#phylogenetic-construction) | [Bacteria](../../workflows_overview/workflows_kingdom.md/#bacteria) | PHB v2.2.0 | Yes; some optional features incompatible | Set-level |
+| [Phylogenetic Construction](../../workflows_overview/workflows_type.md/#phylogenetic-construction) | [Bacteria](../../workflows_overview/workflows_kingdom.md/#bacteria) | PHB v2.3.0 | Yes; some optional features incompatible | Set-level |
 
 ## Snippy_Streamline_PHB
 
diff --git a/docs/workflows/phylogenetic_construction/snippy_streamline_fasta.md b/docs/workflows/phylogenetic_construction/snippy_streamline_fasta.md
index 890674b3f..118c66588 100644
--- a/docs/workflows/phylogenetic_construction/snippy_streamline_fasta.md
+++ b/docs/workflows/phylogenetic_construction/snippy_streamline_fasta.md
@@ -4,7 +4,7 @@
 
 | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** |
 |---|---|---|---|---|
-| [Phylogenetic Construction](../../workflows_overview/workflows_type.md/#phylogenetic-construction) | [Bacteria](../../workflows_overview/workflows_kingdom.md/#bacteria) | PHB v2.2.0 | Yes; some optional features incompatible | Set-level |
+| [Phylogenetic Construction](../../workflows_overview/workflows_type.md/#phylogenetic-construction) | [Bacteria](../../workflows_overview/workflows_kingdom.md/#bacteria) | PHB v2.3.0 | Yes; some optional features incompatible | Set-level |
 
 ## Snippy_Streamline_FASTA_PHB
 
diff --git a/docs/workflows/public_data_sharing/fetch_srr_accession.md b/docs/workflows/public_data_sharing/fetch_srr_accession.md
index aa18c6438..df432d1ca 100644
--- a/docs/workflows/public_data_sharing/fetch_srr_accession.md
+++ b/docs/workflows/public_data_sharing/fetch_srr_accession.md
@@ -4,7 +4,7 @@
 
 | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** |
 |---|---|---|---|---|
-| [Public Data Sharing](../../workflows_overview/workflows_type.md/#public-data-sharing) | [Any Taxa](../../workflows_overview/workflows_kingdom.md/#any-taxa) | PHB v2.3.0 | Yes | Sample-level |
+| [Data Import](../../workflows_overview/workflows_type.md/#data-import) | [Any Taxa](../../workflows_overview/workflows_kingdom.md/#any-taxa) | PHB v2.3.0 | Yes | Sample-level |
 
 ## Fetch SRR Accession
 
diff --git a/docs/workflows/public_data_sharing/mercury_prep_n_batch.md b/docs/workflows/public_data_sharing/mercury_prep_n_batch.md
index 4fcc48d36..56e169e82 100644
--- a/docs/workflows/public_data_sharing/mercury_prep_n_batch.md
+++ b/docs/workflows/public_data_sharing/mercury_prep_n_batch.md
@@ -4,7 +4,7 @@
 
 | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** |
 |---|---|---|---|---|
-| [Public Data Sharing](../../workflows_overview/workflows_type.md/#public-data-sharing) | [Viral](../../workflows_overview/workflows_kingdom.md/#viral) | PHB v2.2.0 | Yes | Set-level |
+| [Public Data Sharing](../../workflows_overview/workflows_type.md/#public-data-sharing) | [Viral](../../workflows_overview/workflows_kingdom.md/#viral) | PHB v2.3.0 | Yes | Set-level |
 
 ## Mercury_Prep_N_Batch_PHB
 
diff --git a/docs/workflows/public_data_sharing/terra_2_ncbi.md b/docs/workflows/public_data_sharing/terra_2_ncbi.md
index 0fa48e50e..54e17aa9d 100644
--- a/docs/workflows/public_data_sharing/terra_2_ncbi.md
+++ b/docs/workflows/public_data_sharing/terra_2_ncbi.md
@@ -4,7 +4,7 @@
 
 | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** |
 |---|---|---|---|---|
-| [Public Data Sharing](../../workflows_overview/workflows_type.md/#public-data-sharing) | [Bacteria](../../workflows_overview/workflows_kingdom.md#bacteria), [Mycotics](../../workflows_overview/workflows_kingdom.md#mycotics) [Viral](../../workflows_overview/workflows_kingdom.md/#viral) | PHB v2.1.0 | No | Set-level |
+| [Public Data Sharing](../../workflows_overview/workflows_type.md/#public-data-sharing) | [Bacteria](../../workflows_overview/workflows_kingdom.md#bacteria), [Mycotics](../../workflows_overview/workflows_kingdom.md#mycotics) [Viral](../../workflows_overview/workflows_kingdom.md/#viral) | PHB v2.3.0 | No | Set-level |
 
 ## Terra_2_NCBI_PHB
 
diff --git a/docs/workflows/standalone/concatenate_illumina_lanes.md b/docs/workflows/standalone/concatenate_illumina_lanes.md
new file mode 100644
index 000000000..282844fa4
--- /dev/null
+++ b/docs/workflows/standalone/concatenate_illumina_lanes.md
@@ -0,0 +1,47 @@
+# Concatenate Illumina Lanes
+
+## Quick Facts
+
+| **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** |
+|---|---|---|---|---|
+| [Standalone](../../workflows_overview/workflows_type.md/#standalone) | [Any Taxa](../../workflows_overview/workflows_kingdom.md/#any-taxa) | PHB 2.3.0 | Yes | Sample-level |
+
+## Concatenate_Illumina_Lanes_PHB
+
+Some Illumina machines produce multi-lane FASTQ files for a single sample. This workflow concatenates the multiple lanes into a single FASTQ file per read type (forward or reverse).
+
+### Inputs
+
+| **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** |
+|---|---|---|---|---|---|
+| concatenate_illumina_lanes | **read1_lane1** | File | The first lane for the forward reads | | Required |
+| concatenate_illumina_lanes | **read1_lane2** | File | The second lane for the forward reads | | Required |
+| concatenate_illumina_lanes | **samplename** | String | The name of the sample, used to name the output files | | Required |
+| cat_lanes | **cpu** | Int | Number of CPUs to allocate to the task | 2 | Optional |
+| cat_lanes | **disk_size** | Int | Amount of storage (in GB) to allocate to the task | 50 | Optional |
+| cat_lanes | **docker** | String | The Docker container to use for the task |  "us-docker.pkg.dev/general-theiagen/theiagen/utility:1.2" | Optional |
+| cat_lanes | **memory** | Int | Amount of memory/RAM (in GB) to allocate to the task | 4 | Optional |
+| concatenate_illumina_lanes | **read1_lane3** | File | The third lane for the forward reads | | Optional |
+| concatenate_illumina_lanes | **read1_lane4** | File | The fourth lane for the forward reads | | Optional |
+| concatenate_illumina_lanes | **read2_lane1** | File | The first lane for the reverse reads | | Optional |
+| concatenate_illumina_lanes | **read2_lane2** | File | The second lane for the reverse reads | | Optional |
+| concatenate_illumina_lanes | **read2_lane3** | File | The third lane for the reverse reads | | Optional |
+| concatenate_illumina_lanes | **read2_lane4** | File | The fourth lane for the reverse reads | | 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 |
+
+### Workflow Tasks
+
+This workflow concatenates the Illumina lanes for forward and (if provided) reverse reads. The output files are named as followed:
+
+- Forward reads: `<samplename>_merged_R1.fastq.gz`
+- Reverse reads: `<samplename>_merged_R2.fastq.gz`
+
+### Outputs
+
+| **Variable** | **Type** | **Description** |
+|---|---|---|
+| concatenate_illumina_lanes_analysis_date | String | Date of analysis |
+| concatenate_illumina_lanes_version | String | Version of PHB used for the analysis |
+| read1_concatenated | File | Concatenated forward reads |
+| read2_concatenated | File | Concatenated reverse reads |
diff --git a/docs/workflows/standalone/kraken2.md b/docs/workflows/standalone/kraken2.md
index df36e56a1..95c86c216 100644
--- a/docs/workflows/standalone/kraken2.md
+++ b/docs/workflows/standalone/kraken2.md
@@ -4,7 +4,7 @@
 
 | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** |
 |---|---|---|---|---|
-| [Standalone](../../workflows_overview/workflows_type.md/#standalone) | [Any Taxa](../../workflows_overview/workflows_kingdom.md/#any-taxa) | PHB v2.0.0 | Yes | Sample-level |
+| [Standalone](../../workflows_overview/workflows_type.md/#standalone) | [Any Taxa](../../workflows_overview/workflows_kingdom.md/#any-taxa) | PHB v2.3.0 | Yes | Sample-level |
 
 ## Kraken2 Workflows
 
diff --git a/docs/workflows/standalone/tbprofiler_tngs.md b/docs/workflows/standalone/tbprofiler_tngs.md
index d0061fdd7..96f29e0bf 100644
--- a/docs/workflows/standalone/tbprofiler_tngs.md
+++ b/docs/workflows/standalone/tbprofiler_tngs.md
@@ -4,7 +4,7 @@
 
 | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** |
 |---|---|---|---|---|
-| [Standalone](../../workflows_overview/workflows_type.md/#standalone) | [Bacteria](../../workflows_overview/workflows_kingdom.md/#bacteria) | PHB v2.0.0 | Yes | Sample-level |
+| [Standalone](../../workflows_overview/workflows_type.md/#standalone) | [Bacteria](../../workflows_overview/workflows_kingdom.md/#bacteria) | PHB v2.3.0 | Yes | Sample-level |
 
 ## TBProfiler_tNGS_PHB
 
@@ -23,7 +23,7 @@ This workflow is still in experimental research stages. Documentation is minimal
 | tbp_parser | **coverage_threshold** | Int | The minimum percentage of a region to exceed the minimum depth for a region to pass QC in tbp_parser | 100 | Optional |
 | tbp_parser | **cpu** | Int | Number of CPUs to allocate to the task | 1 | Optional |
 | tbp_parser | **disk_size** | Int | Amount of storage (in GB) to allocate to the task | 100 | Optional |
-| tbp_parser | **docker** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:1.6.0 | Optional |
+| tbp_parser | **docker** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:2.1.1 | Optional |
 | tbp_parser | **etha237_frequency** | Float | Minimum frequency for a mutation in ethA at protein position 237 to pass QC in tbp-parser | 0.1 | Optional |
 | tbp_parser | **expert_rule_regions_bed** | File | A file that contains the regions where R mutations and expert rules are applied |  | Optional |
 | tbp_parser | **memory** | Int | Amount of memory/RAM (in GB) to allocate to the task | 4 | Optional |
diff --git a/docs/workflows_overview/workflows_alphabetically.md b/docs/workflows_overview/workflows_alphabetically.md
index c937e815b..cc90bf439 100644
--- a/docs/workflows_overview/workflows_alphabetically.md
+++ b/docs/workflows_overview/workflows_alphabetically.md
@@ -11,44 +11,46 @@ title: Alphabetical Workflows
 | **Name** | **Description** | **Applicable Kingdom** | **Workflow Level** | **Command-line Compatibility**[^1] | **Last Known Changes** | **Dockstore** |
 |---|---|---|---|---|---|---|
 | [**Assembly_Fetch**](../workflows/data_import/assembly_fetch.md) | Download assemblies from NCBI, after optionally identifying the closest RefSeq reference genome to your own draft assembly | Any taxa | Sample-level | Yes | v1.3.0 | [Assembly_Fetch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Assembly_Fetch_PHB:main?tab=info) |
-| [**Augur**](../workflows/phylogenetic_construction/augur.md) | Phylogenetic analysis for viral pathogens | Viral | Sample-level, Set-level | Yes | v2.1.0 | [Augur_Prep_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Augur_Prep_PHB:main?tab=info), [Augur_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Augur_PHB:main?tab=info) |
+| [**Augur**](../workflows/phylogenetic_construction/augur.md) | Phylogenetic analysis for viral pathogens | Viral | Sample-level, Set-level | Yes | v2.3.0 | [Augur_Prep_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Augur_Prep_PHB:main?tab=info), [Augur_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Augur_PHB:main?tab=info) |
 | [**BaseSpace_Fetch**](../workflows/data_import/basespace_fetch.md)| Import data from BaseSpace into Terra | Any taxa | Sample-level | Yes | v2.0.0 | [BaseSpace_Fetch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/BaseSpace_Fetch_PHB:main?tab=info) |
 | [**Cauris_CladeTyper**](../workflows/standalone/cauris_cladetyper.md)| C. auris clade assignment | Mycotics | Sample-level | Yes | v1.0.0 | [Cauris_CladeTyper_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Cauris_CladeTyper_PHB:main?tab=info) |
 | [**Concatenate_Column_Content**](../workflows/data_export/concatenate_column_content.md) | Concatenate contents of a specified Terra data table column for many samples ("entities") | Any taxa | Set-level | Yes | v2.1.0 | [Concatenate_Column_Content_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Concatenate_Column_Content_PHB:main?tab=info) |
+| [**Concatenate_Illumina_Lanes**](../workflows/standalone/concatenate_illumina_lanes.md)| Concatenate Illumina lanes for a single sample | Any taxa | Sample-level | Yes | v2.3.0 | [Concatenate_Illumina_Lanes_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Concatenate_Illumina_Lanes_PHB:main?tab=info) |
 | [**Core_Gene_SNP**](../workflows/phylogenetic_construction/core_gene_snp.md) | Pangenome analysis | Bacteria | Set-level | Some optional features incompatible, Yes | v2.1.0 | [Core_Gene_SNP_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Core_Gene_SNP_PHB:main?tab=info) |
 | [**Create_Terra_Table**](../workflows/data_import/create_terra_table.md)| Upload data to Terra and then run this workflow to have the table automatically created | Any taxa | | Yes | v2.2.0 | [Create_Terra_Table_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Create_Terra_Table_PHB:main?tab=info) |
 | [**CZGenEpi_Prep**](../workflows/phylogenetic_construction/czgenepi_prep.md)| Prepare metadata and fasta files for easy upload to the CZ GEN EPI platform. | Monkeypox virus, SARS-CoV-2, Viral | Set-level | No | v1.3.0 | [CZGenEpi_Prep_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/CZGenEpi_Prep_PHB:main?tab=info) |
+| [**Fetch_SRR_Accession**](../workflows/public_data_sharing/fetch_srr_accession.md)| Provided a BioSample accession, identify any associated SRR accession(s) | Any taxa | Sample-level | Yes | v2.3.0 | [*Fetch_SRR_Accession_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Fetch_SRR_Accession_PHB:main?tab=info) |
 | [**Find_Shared_Variants**](../workflows/phylogenetic_construction/find_shared_variants.md)| Combines and reshapes variant data from Snippy_Variants to illustrate variants shared across multiple samples | Bacteria, Mycotics | Set-level | Yes | v2.0.0 | [Find_Shared_Variants_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Find_Shared_Variants_PHB:main?tab=info) |
 | [**Freyja Workflow Series**](../workflows/genomic_characterization/freyja.md)| Recovers relative lineage abundances from mixed sample data and generates visualizations | SARS-CoV-2, Viral | Sample-level, Set-level | Yes | v2.2.0 | [Freyja_FASTQ_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Freyja_FASTQ_PHB:main?tab=info), [Freyja_Plot_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Freyja_Plot_PHB:main?tab=info), [Freyja_Dashboard_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Freyja_Dashboard_PHB:main?tab=info), [Freyja_Update_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Freyja_Update_PHB:main?tab=info) |
 | [**GAMBIT_Query**](../workflows/standalone/gambit_query.md)| Taxon identification of genome assembly using GAMBIT | Bacteria, Mycotics | Sample-level | Yes | v2.0.0 | [Gambit_Query_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Gambit_Query_PHB:main?tab=info) |
-| [**Kraken2**](../workflows/standalone/kraken2.md) | Taxa identification from reads | Any taxa | Sample-level | Yes | v2.0.0 | [Kraken2_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Kraken2_PE_PHB:main?tab=info), [Kraken2_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Kraken2_SE_PHB:main?tab=info) |
+| [**Kraken2**](../workflows/standalone/kraken2.md) | Taxa identification from reads | Any taxa | Sample-level | Yes | v2.3.0 | [Kraken2_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Kraken2_PE_PHB:main?tab=info), [Kraken2_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Kraken2_SE_PHB:main?tab=info) |
 | [**kSNP3**](../workflows/phylogenetic_construction/ksnp3.md)| SNP-based phylogenetic analysis from assemblies | Bacteria, Mycotics, Viral | Set-level | Some optional features incompatible, Yes | v2.1.0 | [kSNP3_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/kSNP3_PHB:main?tab=info) |
 | [**Lyve_SET**](../workflows/phylogenetic_construction/lyve_set.md)| Alignment of reads to a reference genome, SNP calling, curation of high quality SNPs, phylogenetic analysis | Bacteria | Set-level | Yes | v2.1.0 | [Lyve_SET_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Lyve_SET_PHB:main?tab=info) |
 | [**MashTree_FASTA**](../workflows/phylogenetic_construction/mashtree_fasta.md)| Mash-distance based phylogenetic analysis from assemblies | Bacteria, Mycotics, Viral | Set-level | Some optional features incompatible, Yes | v2.1.0 | [MashTree_FASTA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/MashTree_FASTA_PHB:main?tab=info) |
-| [**Mercury_Prep_N_Batch**](../workflows/public_data_sharing/mercury_prep_n_batch.md)| Prepare metadata and sequence data for submission to NCBI and GISAID | Influenza, Monkeypox virus, SARS-CoV-2, Viral | Set-level | No | v2.2.0 | [Mercury_Prep_N_Batch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Mercury_Prep_N_Batch_PHB:main?tab=info) |
+| [**Mercury_Prep_N_Batch**](../workflows/public_data_sharing/mercury_prep_n_batch.md)| Prepare metadata and sequence data for submission to NCBI and GISAID | Influenza, Monkeypox virus, SARS-CoV-2, Viral | Set-level | No | v2.3.0 | [Mercury_Prep_N_Batch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Mercury_Prep_N_Batch_PHB:main?tab=info) |
 | [**NCBI-AMRFinderPlus**](../workflows/standalone/ncbi_amrfinderplus.md)| Runs NCBI's AMRFinderPlus on genome assemblies (bacterial and fungal) | Bacteria, Mycotics | Sample-level | Yes | v2.0.0 | [NCBI-AMRFinderPlus_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/NCBI-AMRFinderPlus_PHB:main?tab=info) |
 | [**NCBI_Scrub**](../workflows/standalone/ncbi_scrub.md)| Runs NCBI's HRRT on Illumina FASTQs | Any taxa | Sample-level | Yes | v2.2.1 | [NCBI_Scrub_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/NCBI_Scrub_PE_PHB:main?tab=info), [NCBI_Scrub_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/NCBI_Scrub_SE_PHB:main?tab=info) |
 | [**Pangolin_Update**](../workflows/genomic_characterization/pangolin_update.md) | Update Pangolin assignments | SARS-CoV-2, Viral | Sample-level | Yes | v2.0.0 | [Pangolin_Update_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Pangolin_Update_PHB:main?tab=info) |
 | [**RASUSA**](../workflows/standalone/rasusa.md)| Randomly subsample sequencing reads to a specified coverage | Any taxa | Sample-level | Yes | v2.0.0 | [RASUSA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/RASUSA_PHB:main?tab=info) |
 | [**Rename_FASTQ**](../workflows/standalone/rename_fastq.md)| Rename paired-end or single-end read files in a Terra data table in a non-destructive way | Any taxa | Sample-level | Yes | v2.1.0 | [Rename_FASTQ_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Rename_FASTQ_PHB:im-utilities-rename-files?tab=info) |
 | [**Samples_to_Ref_Tree**](../workflows/phylogenetic_placement/samples_to_ref_tree.md)| Use Nextclade 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 | [Samples_to_Ref_Tree_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Samples_to_Ref_Tree_PHB:main?tab=info) |
-| [**Snippy_Streamline**](../workflows/phylogenetic_construction/snippy_streamline.md)| Implementation of Snippy workflows for phylogenetic analysis from reads, with optional dynamic reference selection | Bacteria | Set-level | Yes | v2.2.0 | [Snippy_Streamline_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Streamline_PHB:main?tab=info) |
-| [**Snippy_Streamline_FASTA**](../workflows/phylogenetic_construction/snippy_streamline_fasta.md)| Implementation of Snippy workflows for phylogenetic analysis from assembled genomes (in FASTA format), with optional dynamic reference selection | Bacteria | Set-level | Yes | v2.2.0 | [Snippy_Streamline_FASTA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Streamline_FASTA_PHB:im-snippy-fasta-dev?tab=info) |
-| [**Snippy_Tree**](../workflows/phylogenetic_construction/snippy_tree.md)| SNP-based phylogenetic analysis from reads, with option to mask recombination | Bacteria | Set-level | Some optional features incompatible, Yes | v2.1.0 | [Snippy_Tree_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Tree_PHB:main?tab=info) |
-| [**Snippy_Variants**](../workflows/phylogenetic_construction/snippy_variants.md)| Alignment of reads to a reference genome, then SNP calling | Bacteria, Mycotics, Viral | Sample-level | Yes | v2.2.0 | [Snippy_Variants_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Variants_PHB:main?tab=info) |
+| [**Snippy_Streamline**](../workflows/phylogenetic_construction/snippy_streamline.md)| Implementation of Snippy workflows for phylogenetic analysis from reads, with optional dynamic reference selection | Bacteria | Set-level | Yes | v2.3.0 | [Snippy_Streamline_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Streamline_PHB:main?tab=info) |
+| [**Snippy_Streamline_FASTA**](../workflows/phylogenetic_construction/snippy_streamline_fasta.md)| Implementation of Snippy workflows for phylogenetic analysis from assembled genomes (in FASTA format), with optional dynamic reference selection | Bacteria | Set-level | Yes | v2.3.0 | [Snippy_Streamline_FASTA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Streamline_FASTA_PHB:im-snippy-fasta-dev?tab=info) |
+| [**Snippy_Tree**](../workflows/phylogenetic_construction/snippy_tree.md)| SNP-based phylogenetic analysis from reads, with option to mask recombination | Bacteria | Set-level | Some optional features incompatible, Yes | v2.3.0 | [Snippy_Tree_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Tree_PHB:main?tab=info) |
+| [**Snippy_Variants**](../workflows/phylogenetic_construction/snippy_variants.md)| Alignment of reads to a reference genome, then SNP calling | Bacteria, Mycotics, Viral | Sample-level | Yes | v2.3.0 | [Snippy_Variants_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Variants_PHB:main?tab=info) |
 | [**SRA_Fetch**](../workflows/data_import/sra_fetch.md)| Import publicly available reads from SRA using SRR#, ERR# or DRR# | Any taxa | Sample-level | Yes | v2.2.0 | [SRA_Fetch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/SRA_Fetch_PHB:main?tab=info) |
-| [**TBProfiler_tNGS**](../workflows/standalone/tbprofiler_tngs.md)| Performs in silico antimicrobial susceptibility testing on Mycobacterium tuberculosis targeted-NGS samples with TBProfiler and tbp-parser | Bacteria, TB | Sample-level | Yes | v2.0.0 | [TBProfiler_tNGS_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TBProfiler_tNGS_PHB:smw-tngs-tbprofiler-dev?tab=info) |
+| [**TBProfiler_tNGS**](../workflows/standalone/tbprofiler_tngs.md)| Performs in silico antimicrobial susceptibility testing on Mycobacterium tuberculosis targeted-NGS samples with TBProfiler and tbp-parser | Bacteria, TB | Sample-level | Yes | v2.3.0 | [TBProfiler_tNGS_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TBProfiler_tNGS_PHB:smw-tngs-tbprofiler-dev?tab=info) |
 | [**Terra_2_GISAID**](../workflows/public_data_sharing/terra_2_gisaid.md)| Upload of assembly data to GISAID | SARS-CoV-2, Viral | Set-level | Yes | v1.2.1 | [Terra_2_GISAID_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Terra_2_GISAID_PHB:main?tab=info) |
-| [**Terra_2_NCBI**](../workflows/public_data_sharing/terra_2_ncbi.md)| Upload of sequence data to NCBI | Bacteria, Mycotics, Viral | Set-level | No | v2.1.0 | [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 | v2.2.0 | [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) |
-| [**TheiaEuk**](../workflows/genomic_characterization/theiaeuk.md) | Mycotic genome assembly, QC and characterization from WGS data | Mycotics | Sample-level | Some optional features incompatible, Yes | v2.0.1 | [TheiaEuk_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaEuk_Illumina_PE_PHB:main?tab=info) |
-| [**TheiaMeta**](../workflows/genomic_characterization/theiameta.md) | Genome assembly and QC from metagenomic sequencing | Any taxa | Sample-level | Yes | v2.0.0 | [TheiaMeta_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaMeta_Illumina_PE_PHB:main?tab=info) |
-| [**TheiaProk Workflow Series**](../workflows/genomic_characterization/theiaprok.md) | Bacterial genome assembly, QC and characterization from WGS data | Bacteria | Sample-level | Some optional features incompatible, Yes | v2.2.0 | [TheiaProk_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_Illumina_PE_PHB:main?tab=info), [TheiaProk_Illumina_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_Illumina_SE_PHB:main?tab=info), [TheiaProk_ONT_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_ONT_PHB:main?tab=info), [TheiaProk_FASTA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_FASTA_PHB:main?tab=info) |
+| [**Terra_2_NCBI**](../workflows/public_data_sharing/terra_2_ncbi.md)| Upload of sequence data to NCBI | Bacteria, Mycotics, Viral | Set-level | No | v2.3.0 | [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 | v2.3.0 | [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) |
+| [**TheiaEuk**](../workflows/genomic_characterization/theiaeuk.md) | Mycotic genome assembly, QC and characterization from WGS data | Mycotics | Sample-level | Some optional features incompatible, Yes | v2.3.0 | [TheiaEuk_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaEuk_Illumina_PE_PHB:main?tab=info) |
+| [**TheiaMeta**](../workflows/genomic_characterization/theiameta.md) | Genome assembly and QC from metagenomic sequencing | Any taxa | Sample-level | Yes | v2.3.0 | [TheiaMeta_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaMeta_Illumina_PE_PHB:main?tab=info) |
+| [**TheiaProk Workflow Series**](../workflows/genomic_characterization/theiaprok.md) | Bacterial genome assembly, QC and characterization from WGS data | Bacteria | Sample-level | Some optional features incompatible, Yes | v2.3.0 | [TheiaProk_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_Illumina_PE_PHB:main?tab=info), [TheiaProk_Illumina_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_Illumina_SE_PHB:main?tab=info), [TheiaProk_ONT_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_ONT_PHB:main?tab=info), [TheiaProk_FASTA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_FASTA_PHB:main?tab=info) |
 | [**TheiaValidate**](../workflows/standalone/theiavalidate.md)| This workflow performs basic comparisons between user-designated columns in two separate tables. | Any taxa | | No | v2.0.0 | [TheiaValidate_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaValidate_PHB:main?tab=info) |
 | [**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) |
-| [**Fetch_SRR_Accession**](../workflows/public_data_sharing/fetch_srr_accession.md)| Update SRR metadata in a Terra data table at the sample level | Any taxa | | Yes | v2.3.0 | [*Fetch_SRR_Accession_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Fetch_SRR_Accession_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 | v1.2.1 | [VADR_Update_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/VADR_Update_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) |
 | [**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>
diff --git a/docs/workflows_overview/workflows_kingdom.md b/docs/workflows_overview/workflows_kingdom.md
index d10fa2afd..9d8ffc719 100644
--- a/docs/workflows_overview/workflows_kingdom.md
+++ b/docs/workflows_overview/workflows_kingdom.md
@@ -15,16 +15,17 @@ title: Workflows by Kingdom
 | [**Assembly_Fetch**](../workflows/data_import/assembly_fetch.md) | Download assemblies from NCBI, after optionally identifying the closest RefSeq reference genome to your own draft assembly | Any taxa | Sample-level | Yes | v1.3.0 | [Assembly_Fetch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Assembly_Fetch_PHB:main?tab=info) |
 | [**BaseSpace_Fetch**](../workflows/data_import/basespace_fetch.md)| Import data from BaseSpace into Terra | Any taxa | Sample-level | Yes | v2.0.0 | [BaseSpace_Fetch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/BaseSpace_Fetch_PHB:main?tab=info) |
 | [**Concatenate_Column_Content**](../workflows/data_export/concatenate_column_content.md) | Concatenate contents of a specified Terra data table column for many samples ("entities") | Any taxa | Set-level | Yes | v2.1.0 | [Concatenate_Column_Content_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Concatenate_Column_Content_PHB:main?tab=info) |
+| [**Concatenate_Illumina_Lanes**](../workflows/standalone/concatenate_illumina_lanes.md)| Concatenate Illumina lanes for a single sample | Any taxa | Sample-level | Yes | v2.3.0 | [Concatenate_Illumina_Lanes_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Concatenate_Illumina_Lanes_PHB:main?tab=info) |
 | [**Create_Terra_Table**](../workflows/data_import/create_terra_table.md)| Upload data to Terra and then run this workflow to have the table automatically created | Any taxa | | Yes | v2.2.0 | [Create_Terra_Table_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Create_Terra_Table_PHB:main?tab=info) |
-| [**Kraken2**](../workflows/standalone/kraken2.md) | Taxa identification from reads | Any taxa | Sample-level | Yes | v2.0.0 | [Kraken2_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Kraken2_PE_PHB:main?tab=info), [Kraken2_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Kraken2_SE_PHB:main?tab=info) |
+| [**Fetch_SRR_Accession**](../workflows/public_data_sharing/fetch_srr_accession.md)| Provided a BioSample accession, identify any associated SRR accession(s) | Any taxa | Sample-level | Yes | v2.3.0 | [Fetch_SRR_Accession_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Fetch_SRR_Accession_PHB:main?tab=info) |
+| [**Kraken2**](../workflows/standalone/kraken2.md) | Taxa identification from reads | Any taxa | Sample-level | Yes | v2.3.0 | [Kraken2_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Kraken2_PE_PHB:main?tab=info), [Kraken2_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Kraken2_SE_PHB:main?tab=info) |
 | [**NCBI_Scrub**](../workflows/standalone/ncbi_scrub.md)| Runs NCBI's HRRT on Illumina FASTQs | Any taxa | Sample-level | Yes | v2.2.1 | [NCBI_Scrub_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/NCBI_Scrub_PE_PHB:main?tab=info), [NCBI_Scrub_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/NCBI_Scrub_SE_PHB:main?tab=info) |
 | [**RASUSA**](../workflows/standalone/rasusa.md)| Randomly subsample sequencing reads to a specified coverage | Any taxa | Sample-level | Yes | v2.0.0 | [RASUSA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/RASUSA_PHB:main?tab=info) |
 | [**Rename_FASTQ**](../workflows/standalone/rename_fastq.md)| Rename paired-end or single-end read files in a Terra data table in a non-destructive way | Any taxa | Sample-level | Yes | v2.1.0 | [Rename_FASTQ_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Rename_FASTQ_PHB:im-utilities-rename-files?tab=info) |
 | [**SRA_Fetch**](../workflows/data_import/sra_fetch.md)| Import publicly available reads from SRA using SRR#, ERR# or DRR# | Any taxa | Sample-level | Yes | v2.2.0 | [SRA_Fetch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/SRA_Fetch_PHB:main?tab=info) |
-| [**TheiaMeta**](../workflows/genomic_characterization/theiameta.md) | Genome assembly and QC from metagenomic sequencing | Any taxa | Sample-level | Yes | v2.0.0 | [TheiaMeta_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaMeta_Illumina_PE_PHB:main?tab=info) |
+| [**TheiaMeta**](../workflows/genomic_characterization/theiameta.md) | Genome assembly and QC from metagenomic sequencing | Any taxa | Sample-level | Yes | v2.3.0 | [TheiaMeta_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaMeta_Illumina_PE_PHB:main?tab=info) |
 | [**TheiaValidate**](../workflows/standalone/theiavalidate.md)| This workflow performs basic comparisons between user-designated columns in two separate tables. | Any taxa | | No | v2.0.0 | [TheiaValidate_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaValidate_PHB:main?tab=info) |
 | [**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) |
-| [**Fetch_SRR_Accession**](../workflows/public_data_sharing/fetch_srr_accession.md)| Update SRR metadata in a Terra data table at the sample level | Any taxa | Set-level | Yes | v2.3.0 | [Fetch_SRR_Accession_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Fetch_SRR_Accession_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>
@@ -42,13 +43,13 @@ title: Workflows by Kingdom
 | [**Lyve_SET**](../workflows/phylogenetic_construction/lyve_set.md)| Alignment of reads to a reference genome, SNP calling, curation of high quality SNPs, phylogenetic analysis | Bacteria | Set-level | Yes | v2.1.0 | [Lyve_SET_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Lyve_SET_PHB:main?tab=info) |
 | [**MashTree_FASTA**](../workflows/phylogenetic_construction/mashtree_fasta.md)| Mash-distance based phylogenetic analysis from assemblies | Bacteria, Mycotics, Viral | Set-level | Some optional features incompatible, Yes | v2.1.0 | [MashTree_FASTA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/MashTree_FASTA_PHB:main?tab=info) |
 | [**NCBI-AMRFinderPlus**](../workflows/standalone/ncbi_amrfinderplus.md)| Runs NCBI's AMRFinderPlus on genome assemblies (bacterial and fungal) | Bacteria, Mycotics | Sample-level | Yes | v2.0.0 | [NCBI-AMRFinderPlus_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/NCBI-AMRFinderPlus_PHB:main?tab=info) |
-| [**Snippy_Streamline**](../workflows/phylogenetic_construction/snippy_streamline.md)| Implementation of Snippy workflows for phylogenetic analysis from reads, with optional dynamic reference selection | Bacteria | Set-level | Yes | v2.2.0 | [Snippy_Streamline_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Streamline_PHB:main?tab=info) |
-| [**Snippy_Streamline_FASTA**](../workflows/phylogenetic_construction/snippy_streamline_fasta.md)| Implementation of Snippy workflows for phylogenetic analysis from assembled genomes (in FASTA format), with optional dynamic reference selection | Bacteria | Set-level | Yes | v2.2.0 | [Snippy_Streamline_FASTA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Streamline_FASTA_PHB:im-snippy-fasta-dev?tab=info) |
-| [**Snippy_Tree**](../workflows/phylogenetic_construction/snippy_tree.md)| SNP-based phylogenetic analysis from reads, with option to mask recombination | Bacteria | Set-level | Some optional features incompatible, Yes | v2.1.0 | [Snippy_Tree_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Tree_PHB:main?tab=info) |
-| [**Snippy_Variants**](../workflows/phylogenetic_construction/snippy_variants.md)| Alignment of reads to a reference genome, then SNP calling | Bacteria, Mycotics, Viral | Sample-level | Yes | v2.2.0 | [Snippy_Variants_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Variants_PHB:main?tab=info) |
-| [**TBProfiler_tNGS**](../workflows/standalone/tbprofiler_tngs.md)| Performs in silico antimicrobial susceptibility testing on Mycobacterium tuberculosis targeted-NGS samples with TBProfiler and tbp-parser | Bacteria, TB | Sample-level | Yes | v2.0.0 | [TBProfiler_tNGS_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TBProfiler_tNGS_PHB:smw-tngs-tbprofiler-dev?tab=info) |
+| [**Snippy_Streamline**](../workflows/phylogenetic_construction/snippy_streamline.md)| Implementation of Snippy workflows for phylogenetic analysis from reads, with optional dynamic reference selection | Bacteria | Set-level | Yes | v2.3.0 | [Snippy_Streamline_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Streamline_PHB:main?tab=info) |
+| [**Snippy_Streamline_FASTA**](../workflows/phylogenetic_construction/snippy_streamline_fasta.md)| Implementation of Snippy workflows for phylogenetic analysis from assembled genomes (in FASTA format), with optional dynamic reference selection | Bacteria | Set-level | Yes | v2.3.0 | [Snippy_Streamline_FASTA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Streamline_FASTA_PHB:im-snippy-fasta-dev?tab=info) |
+| [**Snippy_Tree**](../workflows/phylogenetic_construction/snippy_tree.md)| SNP-based phylogenetic analysis from reads, with option to mask recombination | Bacteria | Set-level | Some optional features incompatible, Yes | v2.3.0 | [Snippy_Tree_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Tree_PHB:main?tab=info) |
+| [**Snippy_Variants**](../workflows/phylogenetic_construction/snippy_variants.md)| Alignment of reads to a reference genome, then SNP calling | Bacteria, Mycotics, Viral | Sample-level | Yes | v2.3.0 | [Snippy_Variants_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Variants_PHB:main?tab=info) |
+| [**TBProfiler_tNGS**](../workflows/standalone/tbprofiler_tngs.md)| Performs in silico antimicrobial susceptibility testing on Mycobacterium tuberculosis targeted-NGS samples with TBProfiler and tbp-parser | Bacteria, TB | Sample-level | Yes | v2.3.0 | [TBProfiler_tNGS_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TBProfiler_tNGS_PHB:smw-tngs-tbprofiler-dev?tab=info) |
 | [**Terra_2_NCBI**](../workflows/public_data_sharing/terra_2_ncbi.md)| Upload of sequence data to NCBI | Bacteria, Mycotics, Viral | Set-level | No | v2.1.0 | [Terra_2_NCBI_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Terra_2_NCBI_PHB:main?tab=info) |
-| [**TheiaProk Workflow Series**](../workflows/genomic_characterization/theiaprok.md) | Bacterial genome assembly, QC and characterization from WGS data | Bacteria | Sample-level | Some optional features incompatible, Yes | v2.2.0 | [TheiaProk_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_Illumina_PE_PHB:main?tab=info), [TheiaProk_Illumina_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_Illumina_SE_PHB:main?tab=info), [TheiaProk_ONT_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_ONT_PHB:main?tab=info), [TheiaProk_FASTA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_FASTA_PHB:main?tab=info) |
+| [**TheiaProk Workflow Series**](../workflows/genomic_characterization/theiaprok.md) | Bacterial genome assembly, QC and characterization from WGS data | Bacteria | Sample-level | Some optional features incompatible, Yes | v2.3.0 | [TheiaProk_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_Illumina_PE_PHB:main?tab=info), [TheiaProk_Illumina_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_Illumina_SE_PHB:main?tab=info), [TheiaProk_ONT_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_ONT_PHB:main?tab=info), [TheiaProk_FASTA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_FASTA_PHB:main?tab=info) |
 
 </div>
 
@@ -64,9 +65,9 @@ title: Workflows by Kingdom
 | [**kSNP3**](../workflows/phylogenetic_construction/ksnp3.md)| SNP-based phylogenetic analysis from assemblies | Bacteria, Mycotics, Viral | Set-level | Some optional features incompatible, Yes | v2.1.0 | [kSNP3_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/kSNP3_PHB:main?tab=info) |
 | [**MashTree_FASTA**](../workflows/phylogenetic_construction/mashtree_fasta.md)| Mash-distance based phylogenetic analysis from assemblies | Bacteria, Mycotics, Viral | Set-level | Some optional features incompatible, Yes | v2.1.0 | [MashTree_FASTA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/MashTree_FASTA_PHB:main?tab=info) |
 | [**NCBI-AMRFinderPlus**](../workflows/standalone/ncbi_amrfinderplus.md)| Runs NCBI's AMRFinderPlus on genome assemblies (bacterial and fungal) | Bacteria, Mycotics | Sample-level | Yes | v2.0.0 | [NCBI-AMRFinderPlus_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/NCBI-AMRFinderPlus_PHB:main?tab=info) |
-| [**Snippy_Variants**](../workflows/phylogenetic_construction/snippy_variants.md)| Alignment of reads to a reference genome, then SNP calling | Bacteria, Mycotics, Viral | Sample-level | Yes | v2.2.0 | [Snippy_Variants_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Variants_PHB:main?tab=info) |
-| [**Terra_2_NCBI**](../workflows/public_data_sharing/terra_2_ncbi.md)| Upload of sequence data to NCBI | Bacteria, Mycotics, Viral | Set-level | No | v2.1.0 | [Terra_2_NCBI_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Terra_2_NCBI_PHB:main?tab=info) |
-| [**TheiaEuk**](../workflows/genomic_characterization/theiaeuk.md) | Mycotic genome assembly, QC and characterization from WGS data | Mycotics | Sample-level | Some optional features incompatible, Yes | v2.0.1 | [TheiaEuk_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaEuk_Illumina_PE_PHB:main?tab=info) |
+| [**Snippy_Variants**](../workflows/phylogenetic_construction/snippy_variants.md)| Alignment of reads to a reference genome, then SNP calling | Bacteria, Mycotics, Viral | Sample-level | Yes | v2.3.0 | [Snippy_Variants_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Variants_PHB:main?tab=info) |
+| [**Terra_2_NCBI**](../workflows/public_data_sharing/terra_2_ncbi.md)| Upload of sequence data to NCBI | Bacteria, Mycotics, Viral | Set-level | No | v2.3.0 | [Terra_2_NCBI_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Terra_2_NCBI_PHB:main?tab=info) |
+| [**TheiaEuk**](../workflows/genomic_characterization/theiaeuk.md) | Mycotic genome assembly, QC and characterization from WGS data | Mycotics | Sample-level | Some optional features incompatible, Yes | v2.3.0 | [TheiaEuk_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaEuk_Illumina_PE_PHB:main?tab=info) |
 
 </div>
 
@@ -76,20 +77,20 @@ title: Workflows by Kingdom
 
 | **Name** | **Description** | **Applicable Kingdom** | **Workflow Level** | **Command-line Compatibility**[^1] | **Last Known Changes** | **Dockstore** |
 |---|---|---|---|---|---|---|
-| [**Augur**](../workflows/phylogenetic_construction/augur.md) | Phylogenetic analysis for viral pathogens | Viral | Sample-level, Set-level | Yes | v2.1.0 | [Augur_Prep_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Augur_Prep_PHB:main?tab=info), [Augur_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Augur_PHB:main?tab=info) |
+| [**Augur**](../workflows/phylogenetic_construction/augur.md) | Phylogenetic analysis for viral pathogens | Viral | Sample-level, Set-level | Yes | v2.3.0 | [Augur_Prep_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Augur_Prep_PHB:main?tab=info), [Augur_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Augur_PHB:main?tab=info) |
 | [**CZGenEpi_Prep**](../workflows/phylogenetic_construction/czgenepi_prep.md)| Prepare metadata and fasta files for easy upload to the CZ GEN EPI platform. | Monkeypox virus, SARS-CoV-2, Viral | Set-level | No | v1.3.0 | [CZGenEpi_Prep_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/CZGenEpi_Prep_PHB:main?tab=info) |
-| [**Freyja Workflow Series**](../workflows/genomic_characterization/freyja.md)| Recovers relative lineage abundances from mixed sample data and generates visualizations | SARS-CoV-2, Viral | Sample-level, Set-level | Yes | v2.2.0 | [Freyja_FASTQ_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Freyja_FASTQ_PHB:main?tab=info), [Freyja_Plot_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Freyja_Plot_PHB:main?tab=info), [Freyja_Dashboard_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Freyja_Dashboard_PHB:main?tab=info), [Freyja_Update_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Freyja_Update_PHB:main?tab=info) |
+| [**Freyja Workflow Series**](../workflows/genomic_characterization/freyja.md)| Recovers relative lineage abundances from mixed sample data and generates visualizations | SARS-CoV-2, Viral | Sample-level, Set-level | Yes | v2.3.0 | [Freyja_FASTQ_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Freyja_FASTQ_PHB:main?tab=info), [Freyja_Plot_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Freyja_Plot_PHB:main?tab=info), [Freyja_Dashboard_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Freyja_Dashboard_PHB:main?tab=info), [Freyja_Update_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Freyja_Update_PHB:main?tab=info) |
 | [**kSNP3**](../workflows/phylogenetic_construction/ksnp3.md)| SNP-based phylogenetic analysis from assemblies | Bacteria, Mycotics, Viral | Set-level | Some optional features incompatible, Yes | v2.1.0 | [kSNP3_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/kSNP3_PHB:main?tab=info) |
 | [**MashTree_FASTA**](../workflows/phylogenetic_construction/mashtree_fasta.md)| Mash-distance based phylogenetic analysis from assemblies | Bacteria, Mycotics, Viral | Set-level | Some optional features incompatible, Yes | v2.1.0 | [MashTree_FASTA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/MashTree_FASTA_PHB:main?tab=info) |
-| [**Mercury_Prep_N_Batch**](../workflows/public_data_sharing/mercury_prep_n_batch.md)| Prepare metadata and sequence data for submission to NCBI and GISAID | Influenza, Monkeypox virus, SARS-CoV-2, Viral | Set-level | No | v2.2.0 | [Mercury_Prep_N_Batch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Mercury_Prep_N_Batch_PHB:main?tab=info) |
+| [**Mercury_Prep_N_Batch**](../workflows/public_data_sharing/mercury_prep_n_batch.md)| Prepare metadata and sequence data for submission to NCBI and GISAID | Influenza, Monkeypox virus, SARS-CoV-2, Viral | Set-level | No | v2.3.0 | [Mercury_Prep_N_Batch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Mercury_Prep_N_Batch_PHB:main?tab=info) |
 | [**Pangolin_Update**](../workflows/genomic_characterization/pangolin_update.md) | Update Pangolin assignments | SARS-CoV-2, Viral | Sample-level | Yes | v2.0.0 | [Pangolin_Update_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Pangolin_Update_PHB:main?tab=info) |
 | [**Samples_to_Ref_Tree**](../workflows/phylogenetic_placement/samples_to_ref_tree.md)| Use Nextclade 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 | [Samples_to_Ref_Tree_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Samples_to_Ref_Tree_PHB:main?tab=info) |
-| [**Snippy_Variants**](../workflows/phylogenetic_construction/snippy_variants.md)| Alignment of reads to a reference genome, then SNP calling | Bacteria, Mycotics, Viral | Sample-level | Yes | v2.2.0 | [Snippy_Variants_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Variants_PHB:main?tab=info) |
+| [**Snippy_Variants**](../workflows/phylogenetic_construction/snippy_variants.md)| Alignment of reads to a reference genome, then SNP calling | Bacteria, Mycotics, Viral | Sample-level | Yes | v2.3.0 | [Snippy_Variants_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Variants_PHB:main?tab=info) |
 | [**Terra_2_GISAID**](../workflows/public_data_sharing/terra_2_gisaid.md)| Upload of assembly data to GISAID | SARS-CoV-2, Viral | Set-level | Yes | v1.2.1 | [Terra_2_GISAID_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Terra_2_GISAID_PHB:main?tab=info) |
-| [**Terra_2_NCBI**](../workflows/public_data_sharing/terra_2_ncbi.md)| Upload of sequence data to NCBI | Bacteria, Mycotics, Viral | Set-level | No | v2.1.0 | [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 | v2.2.0 | [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) |
+| [**Terra_2_NCBI**](../workflows/public_data_sharing/terra_2_ncbi.md)| Upload of sequence data to NCBI | Bacteria, Mycotics, Viral | Set-level | No | v2.3.0 | [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 | v2.3.0 | [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 | v1.2.1 | [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) |
 
 </div>
 
diff --git a/docs/workflows_overview/workflows_type.md b/docs/workflows_overview/workflows_type.md
index 14f23fd92..e43a3f7c0 100644
--- a/docs/workflows_overview/workflows_type.md
+++ b/docs/workflows_overview/workflows_type.md
@@ -15,6 +15,7 @@ title: Workflows by Type
 | [**Assembly_Fetch**](../workflows/data_import/assembly_fetch.md) | Download assemblies from NCBI, after optionally identifying the closest RefSeq reference genome to your own draft assembly | Any taxa | Sample-level | Yes | v1.3.0 | [Assembly_Fetch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Assembly_Fetch_PHB:main?tab=info) |
 | [**BaseSpace_Fetch**](../workflows/data_import/basespace_fetch.md)| Import data from BaseSpace into Terra | Any taxa | Sample-level | Yes | v2.0.0 | [BaseSpace_Fetch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/BaseSpace_Fetch_PHB:main?tab=info) |
 | [**Create_Terra_Table**](../workflows/data_import/create_terra_table.md)| Upload data to Terra and then run this workflow to have the table automatically created | Any taxa | | Yes | v2.2.0 | [Create_Terra_Table_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Create_Terra_Table_PHB:main?tab=info) |
+| [**Fetch_SRR_Accession**](../workflows/public_data_sharing/fetch_srr_accession.md)| Provided a BioSample accession, identify any associated SRR accession(s) | Any taxa | Sample-level | Yes | v2.3.0 | [Fetch_SRR_Accession_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Fetch_SRR_Accession_PHB:main?tab=info) |
 | [**SRA_Fetch**](../workflows/data_import/sra_fetch.md)| Import publicly available reads from SRA using SRR#, ERR# or DRR# | Any taxa | Sample-level | Yes | v2.2.0 | [SRA_Fetch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/SRA_Fetch_PHB:main?tab=info) |
 
 </div>
@@ -25,13 +26,13 @@ title: Workflows by Type
 
 | **Name** | **Description** | **Applicable Kingdom** | **Workflow Level** | **Command-line Compatibility**[^1] | **Last Known Changes** | **Dockstore** |
 |---|---|---|---|---|---|---|
-| [**Freyja Workflow Series**](../workflows/genomic_characterization/freyja.md)| Recovers relative lineage abundances from mixed sample data and generates visualizations | SARS-CoV-2, Viral | Sample-level, Set-level | Yes | v2.2.0 | [Freyja_FASTQ_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Freyja_FASTQ_PHB:main?tab=info), [Freyja_Plot_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Freyja_Plot_PHB:main?tab=info), [Freyja_Dashboard_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Freyja_Dashboard_PHB:main?tab=info), [Freyja_Update_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Freyja_Update_PHB:main?tab=info) |
+| [**Freyja Workflow Series**](../workflows/genomic_characterization/freyja.md)| Recovers relative lineage abundances from mixed sample data and generates visualizations | SARS-CoV-2, Viral | Sample-level, Set-level | Yes | v2.3.0 | [Freyja_FASTQ_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Freyja_FASTQ_PHB:main?tab=info), [Freyja_Plot_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Freyja_Plot_PHB:main?tab=info), [Freyja_Dashboard_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Freyja_Dashboard_PHB:main?tab=info), [Freyja_Update_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Freyja_Update_PHB:main?tab=info) |
 | [**Pangolin_Update**](../workflows/genomic_characterization/pangolin_update.md) | Update Pangolin assignments | SARS-CoV-2, Viral | Sample-level | Yes | v2.0.0 | [Pangolin_Update_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Pangolin_Update_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 | v2.2.0 | [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) |
-| [**TheiaEuk**](../workflows/genomic_characterization/theiaeuk.md) | Mycotic genome assembly, QC and characterization from WGS data | Mycotics | Sample-level | Some optional features incompatible, Yes | v2.0.1 | [TheiaEuk_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaEuk_Illumina_PE_PHB:main?tab=info) |
-| [**TheiaMeta**](../workflows/genomic_characterization/theiameta.md) | Genome assembly and QC from metagenomic sequencing | Any taxa | Sample-level | Yes | v2.0.0 | [TheiaMeta_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaMeta_Illumina_PE_PHB:main?tab=info) |
-| [**TheiaProk Workflow Series**](../workflows/genomic_characterization/theiaprok.md) | Bacterial genome assembly, QC and characterization from WGS data | Bacteria | Sample-level | Some optional features incompatible, Yes | v2.2.0 | [TheiaProk_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_Illumina_PE_PHB:main?tab=info), [TheiaProk_Illumina_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_Illumina_SE_PHB:main?tab=info), [TheiaProk_ONT_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_ONT_PHB:main?tab=info), [TheiaProk_FASTA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_FASTA_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 | v1.2.1 | [VADR_Update_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/VADR_Update_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 | v2.3.0 | [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) |
+| [**TheiaEuk**](../workflows/genomic_characterization/theiaeuk.md) | Mycotic genome assembly, QC and characterization from WGS data | Mycotics | Sample-level | Some optional features incompatible, Yes | v2.3.0 | [TheiaEuk_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaEuk_Illumina_PE_PHB:main?tab=info) |
+| [**TheiaMeta**](../workflows/genomic_characterization/theiameta.md) | Genome assembly and QC from metagenomic sequencing | Any taxa | Sample-level | Yes | v2.3.0 | [TheiaMeta_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaMeta_Illumina_PE_PHB:main?tab=info) |
+| [**TheiaProk Workflow Series**](../workflows/genomic_characterization/theiaprok.md) | Bacterial genome assembly, QC and characterization from WGS data | Bacteria | Sample-level | Some optional features incompatible, Yes | v2.3.0 | [TheiaProk_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_Illumina_PE_PHB:main?tab=info), [TheiaProk_Illumina_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_Illumina_SE_PHB:main?tab=info), [TheiaProk_ONT_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_ONT_PHB:main?tab=info), [TheiaProk_FASTA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_FASTA_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 | v2.2.1 | [VADR_Update_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/VADR_Update_PHB:main?tab=info) |
 
 </div>
 
@@ -41,17 +42,17 @@ title: Workflows by Type
 
 | **Name** | **Description** | **Applicable Kingdom** | **Workflow Level** | **Command-line Compatibility**[^1] | **Last Known Changes** | **Dockstore** |
 |---|---|---|---|---|---|---|
-| [**Augur**](../workflows/phylogenetic_construction/augur.md) | Phylogenetic analysis for viral pathogens | Viral | Sample-level, Set-level | Yes | v2.1.0 | [Augur_Prep_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Augur_Prep_PHB:main?tab=info), [Augur_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Augur_PHB:main?tab=info) |
+| [**Augur**](../workflows/phylogenetic_construction/augur.md) | Phylogenetic analysis for viral pathogens | Viral | Sample-level, Set-level | Yes | v2.3.0 | [Augur_Prep_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Augur_Prep_PHB:main?tab=info), [Augur_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Augur_PHB:main?tab=info) |
 | [**Core_Gene_SNP**](../workflows/phylogenetic_construction/core_gene_snp.md) | Pangenome analysis | Bacteria | Set-level | Some optional features incompatible, Yes | v2.1.0 | [Core_Gene_SNP_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Core_Gene_SNP_PHB:main?tab=info) |
 | [**CZGenEpi_Prep**](../workflows/phylogenetic_construction/czgenepi_prep.md)| Prepare metadata and fasta files for easy upload to the CZ GEN EPI platform. | Monkeypox virus, SARS-CoV-2, Viral | Set-level | No | v1.3.0 | [CZGenEpi_Prep_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/CZGenEpi_Prep_PHB:main?tab=info) |
 | [**Find_Shared_Variants**](../workflows/phylogenetic_construction/find_shared_variants.md)| Combines and reshapes variant data from Snippy_Variants to illustrate variants shared across multiple samples | Bacteria, Mycotics | Set-level | Yes | v2.0.0 | [Find_Shared_Variants_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Find_Shared_Variants_PHB:main?tab=info) |
 | [**kSNP3**](../workflows/phylogenetic_construction/ksnp3.md)| SNP-based phylogenetic analysis from assemblies | Bacteria, Mycotics, Viral | Set-level | Some optional features incompatible, Yes | v2.1.0 | [kSNP3_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/kSNP3_PHB:main?tab=info) |
 | [**Lyve_SET**](../workflows/phylogenetic_construction/lyve_set.md)| Alignment of reads to a reference genome, SNP calling, curation of high quality SNPs, phylogenetic analysis | Bacteria | Set-level | Yes | v2.1.0 | [Lyve_SET_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Lyve_SET_PHB:main?tab=info) |
 | [**MashTree_FASTA**](../workflows/phylogenetic_construction/mashtree_fasta.md)| Mash-distance based phylogenetic analysis from assemblies | Bacteria, Mycotics, Viral | Set-level | Some optional features incompatible, Yes | v2.1.0 | [MashTree_FASTA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/MashTree_FASTA_PHB:main?tab=info) |
-| [**Snippy_Streamline**](../workflows/phylogenetic_construction/snippy_streamline.md)| Implementation of Snippy workflows for phylogenetic analysis from reads, with optional dynamic reference selection | Bacteria | Set-level | Yes | v2.2.0 | [Snippy_Streamline_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Streamline_PHB:main?tab=info) |
-| [**Snippy_Streamline_FASTA**](../workflows/phylogenetic_construction/snippy_streamline_fasta.md)| Implementation of Snippy workflows for phylogenetic analysis from assembled genomes (in FASTA format), with optional dynamic reference selection | Bacteria | Set-level | Yes | v2.2.0 | [Snippy_Streamline_FASTA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Streamline_FASTA_PHB:im-snippy-fasta-dev?tab=info) |
-| [**Snippy_Tree**](../workflows/phylogenetic_construction/snippy_tree.md)| SNP-based phylogenetic analysis from reads, with option to mask recombination | Bacteria | Set-level | Some optional features incompatible, Yes | v2.1.0 | [Snippy_Tree_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Tree_PHB:main?tab=info) |
-| [**Snippy_Variants**](../workflows/phylogenetic_construction/snippy_variants.md)| Alignment of reads to a reference genome, then SNP calling | Bacteria, Mycotics, Viral | Sample-level | Yes | v2.2.0 | [Snippy_Variants_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Variants_PHB:main?tab=info) |
+| [**Snippy_Streamline**](../workflows/phylogenetic_construction/snippy_streamline.md)| Implementation of Snippy workflows for phylogenetic analysis from reads, with optional dynamic reference selection | Bacteria | Set-level | Yes | v2.3.0 | [Snippy_Streamline_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Streamline_PHB:main?tab=info) |
+| [**Snippy_Streamline_FASTA**](../workflows/phylogenetic_construction/snippy_streamline_fasta.md)| Implementation of Snippy workflows for phylogenetic analysis from assembled genomes (in FASTA format), with optional dynamic reference selection | Bacteria | Set-level | Yes | v2.3.0 | [Snippy_Streamline_FASTA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Streamline_FASTA_PHB:im-snippy-fasta-dev?tab=info) |
+| [**Snippy_Tree**](../workflows/phylogenetic_construction/snippy_tree.md)| SNP-based phylogenetic analysis from reads, with option to mask recombination | Bacteria | Set-level | Some optional features incompatible, Yes | v2.3.0 | [Snippy_Tree_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Tree_PHB:main?tab=info) |
+| [**Snippy_Variants**](../workflows/phylogenetic_construction/snippy_variants.md)| Alignment of reads to a reference genome, then SNP calling | Bacteria, Mycotics, Viral | Sample-level | Yes | v2.3.0 | [Snippy_Variants_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Variants_PHB:main?tab=info) |
 
 </div>
 
@@ -72,10 +73,9 @@ title: Workflows by Type
 
 | **Name** | **Description** | **Applicable Kingdom** | **Workflow Level** | **Command-line Compatibility**[^1] | **Last Known Changes** | **Dockstore** |
 |---|---|---|---|---|---|---|
-| [**Mercury_Prep_N_Batch**](../workflows/public_data_sharing/mercury_prep_n_batch.md)| Prepare metadata and sequence data for submission to NCBI and GISAID | Influenza, Monkeypox virus, SARS-CoV-2, Viral | Set-level | No | v2.2.0 | [Mercury_Prep_N_Batch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Mercury_Prep_N_Batch_PHB:main?tab=info) |
+| [**Mercury_Prep_N_Batch**](../workflows/public_data_sharing/mercury_prep_n_batch.md)| Prepare metadata and sequence data for submission to NCBI and GISAID | Influenza, Monkeypox virus, SARS-CoV-2, Viral | Set-level | No | v2.3.0 | [Mercury_Prep_N_Batch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Mercury_Prep_N_Batch_PHB:main?tab=info) |
 | [**Terra_2_GISAID**](../workflows/public_data_sharing/terra_2_gisaid.md)| Upload of assembly data to GISAID | SARS-CoV-2, Viral | Set-level | Yes | v1.2.1 | [Terra_2_GISAID_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Terra_2_GISAID_PHB:main?tab=info) |
 | [**Terra_2_NCBI**](../workflows/public_data_sharing/terra_2_ncbi.md)| Upload of sequence data to NCBI | Bacteria, Mycotics, Viral | Set-level | No | v2.1.0 | [Terra_2_NCBI_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Terra_2_NCBI_PHB:main?tab=info) |
-| [**Fetch_SRR_Accession**](../workflows/public_data_sharing/fetch_srr_accession.md)| Update SRR metadata in a Terra data table at the sample level | Any taxa | | Yes | v2.3.0 | [Fetch_SRR_Accession_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Fetch_SRR_Accession_PHB:main?tab=info) |
 
 </div>
 
@@ -98,13 +98,14 @@ title: Workflows by Type
 | **Name** | **Description** | **Applicable Kingdom** | **Workflow Level** | **Command-line Compatibility**[^1] | **Last Known Changes** | **Dockstore** |
 |---|---|---|---|---|---|---|
 | [**Cauris_CladeTyper**](../workflows/standalone/cauris_cladetyper.md)| C. auris clade assignment | Mycotics | Sample-level | Yes | v1.0.0 | [Cauris_CladeTyper_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Cauris_CladeTyper_PHB:main?tab=info) |
+| [**Concatenate_Illumina_Lanes**](../workflows/standalone/concatenate_illumina_lanes.md)| Concatenate Illumina lanes for a single sample | Any taxa | Sample-level | Yes | v2.3.0 | [Concatenate_Illumina_Lanes_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Concatenate_Illumina_Lanes_PHB:main?tab=info) |
 | [**GAMBIT_Query**](../workflows/standalone/gambit_query.md)| Taxon identification of genome assembly using GAMBIT | Bacteria, Mycotics | Sample-level | Yes | v2.0.0 | [Gambit_Query_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Gambit_Query_PHB:main?tab=info) |
-| [**Kraken2**](../workflows/standalone/kraken2.md) | Taxa identification from reads | Any taxa | Sample-level | Yes | v2.0.0 | [Kraken2_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Kraken2_PE_PHB:main?tab=info), [Kraken2_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Kraken2_SE_PHB:main?tab=info) |
+| [**Kraken2**](../workflows/standalone/kraken2.md) | Taxa identification from reads | Any taxa | Sample-level | Yes | v2.3.0 | [Kraken2_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Kraken2_PE_PHB:main?tab=info), [Kraken2_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Kraken2_SE_PHB:main?tab=info) |
 | [**NCBI-AMRFinderPlus**](../workflows/standalone/ncbi_amrfinderplus.md)| Runs NCBI's AMRFinderPlus on genome assemblies (bacterial and fungal) | Bacteria, Mycotics | Sample-level | Yes | v2.0.0 | [NCBI-AMRFinderPlus_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/NCBI-AMRFinderPlus_PHB:main?tab=info) |
 | [**NCBI_Scrub**](../workflows/standalone/ncbi_scrub.md)| Runs NCBI's HRRT on Illumina FASTQs | Any taxa | Sample-level | Yes | v2.2.1 | [NCBI_Scrub_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/NCBI_Scrub_PE_PHB:main?tab=info), [NCBI_Scrub_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/NCBI_Scrub_SE_PHB:main?tab=info) |
 | [**RASUSA**](../workflows/standalone/rasusa.md)| Randomly subsample sequencing reads to a specified coverage | Any taxa | Sample-level | Yes | v2.0.0 | [RASUSA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/RASUSA_PHB:main?tab=info) |
 | [**Rename_FASTQ**](../workflows/standalone/rename_fastq.md)| Rename paired-end or single-end read files in a Terra data table in a non-destructive way | Any taxa | Sample-level | Yes | v2.1.0 | [Rename_FASTQ_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Rename_FASTQ_PHB:im-utilities-rename-files?tab=info) |
-| [**TBProfiler_tNGS**](../workflows/standalone/tbprofiler_tngs.md)| Performs in silico antimicrobial susceptibility testing on Mycobacterium tuberculosis targeted-NGS samples with TBProfiler and tbp-parser | Bacteria, TB | Sample-level | Yes | v2.0.0 | [TBProfiler_tNGS_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TBProfiler_tNGS_PHB:smw-tngs-tbprofiler-dev?tab=info) |
+| [**TBProfiler_tNGS**](../workflows/standalone/tbprofiler_tngs.md)| Performs in silico antimicrobial susceptibility testing on Mycobacterium tuberculosis targeted-NGS samples with TBProfiler and tbp-parser | Bacteria, TB | Sample-level | Yes | v2.3.0 | [TBProfiler_tNGS_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TBProfiler_tNGS_PHB:smw-tngs-tbprofiler-dev?tab=info) |
 | [**TheiaValidate**](../workflows/standalone/theiavalidate.md)| This workflow performs basic comparisons between user-designated columns in two separate tables. | Any taxa | | No | v2.0.0 | [TheiaValidate_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaValidate_PHB:main?tab=info) |
 
 </div>
diff --git a/mkdocs.yml b/mkdocs.yml
index 613f81b15..0bb1d3f4f 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -53,6 +53,7 @@ nav:
                - Zip_Column_Content: workflows/data_export/zip_column_content.md
             - Standalone:
                - Cauris_CladeTyper: workflows/standalone/cauris_cladetyper.md
+               - Concatenate_Illumina_Lanes: workflows/standalone/concatenate_illumina_lanes.md
                - GAMBIT_Query: workflows/standalone/gambit_query.md
                - Kraken2: workflows/standalone/kraken2.md
                - NCBI-AMRFinderPlus: workflows/standalone/ncbi_amrfinderplus.md
@@ -66,7 +67,8 @@ nav:
             - Any Taxa:
                - Assembly_Fetch: workflows/data_import/assembly_fetch.md
                - BaseSpace_Fetch: workflows/data_import/basespace_fetch.md
-               - Concatenate_Column_Content: workflows/data_export/concatenate_column_content.md
+               - Concatenate_Column_Content: workflows/data_export/concatenate_column_content.md               
+               - Concatenate_Illumina_Lanes: workflows/standalone/concatenate_illumina_lanes.md
                - Create_Terra_Table: workflows/data_import/create_terra_table.md
                - Kraken2: workflows/standalone/kraken2.md
                - NCBI-Scrub: workflows/standalone/ncbi_scrub.md
@@ -124,6 +126,7 @@ nav:
             - BaseSpace_Fetch: workflows/data_import/basespace_fetch.md
             - Cauris_CladeTyper: workflows/standalone/cauris_cladetyper.md
             - Concatenate_Column_Content: workflows/data_export/concatenate_column_content.md
+            - Concatenate_Illumina_Lanes: workflows/standalone/concatenate_illumina_lanes.md
             - Core_Gene_SNP: workflows/phylogenetic_construction/core_gene_snp.md
             - Create_Terra_Table: workflows/data_import/create_terra_table.md
             - CZGenEpi_Prep: workflows/phylogenetic_construction/czgenepi_prep.md
diff --git a/tasks/quality_control/read_filtering/task_trimmomatic.wdl b/tasks/quality_control/read_filtering/task_trimmomatic.wdl
index e8a246497..42f62559d 100644
--- a/tasks/quality_control/read_filtering/task_trimmomatic.wdl
+++ b/tasks/quality_control/read_filtering/task_trimmomatic.wdl
@@ -40,9 +40,9 @@ task trimmomatic_pe {
     -threads ~{cpu} \
     ~{read1} ~{read2} \
     -baseout ~{samplename}.fastq.gz \
+    "${CROPPING_VAR}" \
     SLIDINGWINDOW:~{trimmomatic_window_size}:~{trimmomatic_quality_trim_score} \
-    MINLEN:~{trimmomatic_min_length} &> ~{samplename}.trim.stats.txt \
-    "${CROPPING_VAR}"
+    MINLEN:~{trimmomatic_min_length} &> ~{samplename}.trim.stats.txt
 
   >>>
   output {
diff --git a/tasks/species_typing/mycobacterium/task_tbp_parser.wdl b/tasks/species_typing/mycobacterium/task_tbp_parser.wdl
index 310ee61fd..60baa0b99 100644
--- a/tasks/species_typing/mycobacterium/task_tbp_parser.wdl
+++ b/tasks/species_typing/mycobacterium/task_tbp_parser.wdl
@@ -9,17 +9,18 @@ task tbp_parser {
 
     String? sequencing_method
     String? operator
+
     Int? min_depth # default 10
-    Int? coverage_threshold # default 100 (--min_percent_coverage)
-    File? coverage_regions_bed
     Float? min_frequency # default 0.1
     Int? min_read_support # default 10
+    
+    Int? coverage_threshold # default 100 (--min_percent_coverage)
+    File? coverage_regions_bed
   
-    Boolean tbp_parser_debug = false
-
     Boolean add_cycloserine_lims = false
-    
+    Boolean tbp_parser_debug = true
     Boolean tngs_data = false    
+
     Float? rrs_frequency # default 0.1
     Int? rrs_read_support # default 10
     Float? rrl_frequency # default 0.1
@@ -27,11 +28,11 @@ task tbp_parser {
     Float? rpob449_frequency # default 0.1
     Float? etha237_frequency # default 0.1
     File? expert_rule_regions_bed
-
-    String docker = "us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:1.6.0"
-    Int disk_size = 100
-    Int memory = 4
+    
     Int cpu = 1
+    Int disk_size = 100   
+    String docker = "us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:2.2.1"
+    Int memory = 4
   }
   command <<<
     # get version
@@ -42,10 +43,10 @@ task tbp_parser {
       ~{"--sequencing_method " + sequencing_method} \
       ~{"--operator " + operator} \
       ~{"--min_depth " + min_depth} \
-      ~{"--min_percent_coverage " + coverage_threshold} \
-      ~{"--coverage_regions " + coverage_regions_bed} \
       ~{"--min_frequency " + min_frequency} \
       ~{"--min_read_support " + min_read_support} \
+      ~{"--min_percent_coverage " + coverage_threshold} \
+      ~{"--coverage_regions " + coverage_regions_bed} \
       ~{"--tngs_expert_regions " + expert_rule_regions_bed} \
       ~{"--rrs_frequency " + rrs_frequency} \
       ~{"--rrs_read_support " + rrs_read_support} \
@@ -63,7 +64,7 @@ task tbp_parser {
     echo 0.0 > AVG_DEPTH
 
     # get genome percent coverage for the entire reference genome length over min_depth
-    genome=$(samtools depth -J ~{tbprofiler_bam} | awk -F "\t" '{if ($3 >= ~{min_depth}) print;}' | wc -l )
+    genome=$(samtools depth -J ~{tbprofiler_bam} | awk -F "\t" -v min_depth=~{min_depth} '{if ($3 >= min_depth) print;}' | wc -l )
     python3 -c "print ( ($genome / 4411532 ) * 100 )" | tee GENOME_PC
 
     # get genome average depth
diff --git a/tasks/species_typing/mycobacterium/task_tbprofiler.wdl b/tasks/species_typing/mycobacterium/task_tbprofiler.wdl
index 21c4f4b15..bc81ce419 100644
--- a/tasks/species_typing/mycobacterium/task_tbprofiler.wdl
+++ b/tasks/species_typing/mycobacterium/task_tbprofiler.wdl
@@ -5,84 +5,74 @@ task tbprofiler {
     File read1
     File? read2
     String samplename
-
-    # logic
     Boolean ont_data = false
-    Boolean tbprofiler_run_custom_db = false
-    File? tbprofiler_custom_db
-    # minimum thresholds
-    Int cov_frac_threshold = 1
-    Float min_af = 0.1
-    Float min_af_pred = 0.1
-    Int min_depth = 10
-    # tool options within tbprofiler
+    
     String mapper = "bwa"
-    String variant_caller = "freebayes"
+    String variant_caller = "gatk"
     String? variant_calling_params
-    # runtime
+    
+    String? additional_parameters # for tbprofiler
+    
+    Int min_depth = 10
+    Float min_af = 0.1
+    
+    File? tbprofiler_custom_db
+    Boolean tbprofiler_run_cdph_db = false
+    Boolean tbprofiler_run_custom_db = false
+    
     Int cpu = 8     
     Int disk_size = 100
-    String docker = "us-docker.pkg.dev/general-theiagen/staphb/tbprofiler:4.4.2"
+    String docker = "us-docker.pkg.dev/general-theiagen/staphb/tbprofiler:6.4.1"
     Int memory = 16
   }
   command <<<
-    # Print and save date
-    date | tee DATE
-
     # Print and save version
     tb-profiler version > VERSION && sed -i -e 's/TBProfiler version //' VERSION && sed -n -i '$p' VERSION
     
     # check if file is non existant or non empty
-    if [ -z "~{read2}" ] || [ ! -s "~{read2}" ] ; then
+    if [ -z "~{read2}" ] || [ ! -s "~{read2}" ]; then
       INPUT_READS="-1 ~{read1}"
     else
       INPUT_READS="-1 ~{read1} -2 ~{read2}"
     fi
-    
-    if [ "~{ont_data}" = true ]; then
-      mode="--platform nanopore"
-      export ont_data="true"
-    else
-      export ont_data="false"
-    fi
 
     # check if new database file is provided and not empty
-    if [ "~{tbprofiler_run_custom_db}" = true ] ; then
-      echo "Found new database file ~{tbprofiler_custom_db}"
-      prefix=$(basename "~{tbprofiler_custom_db}" | sed 's/\.tar\.gz$//')
-      echo "New database will be created with prefix $prefix"
-
-      echo "Inflating the new database..."
-      tar xfv ~{tbprofiler_custom_db}
+    if ~{tbprofiler_run_custom_db}; then
+      if [ ! -s ~{tbprofiler_custom_db} ]; then
+        echo "Custom database file is empty"
+        TBDB=""
+      else
+        echo "Found new database file ~{tbprofiler_custom_db}"
+        prefix=$(basename "~{tbprofiler_custom_db}" | sed 's/\.tar\.gz$//')
+        tar xfv ~{tbprofiler_custom_db}
+        
+        tb-profiler load_library ./"$prefix"/"$prefix"
 
-      tb-profiler load_library ./"$prefix"/"$prefix"
-
-      TBDB="--db $prefix"
-    else
-      TBDB=""
+        TBDB="--db $prefix"
+      fi
+    elif ~{tbprofiler_run_cdph_db}; then
+      tb-profiler update_tbdb --branch CaliforniaDPH
+      TBDB="--db CaliforniaDPH"
     fi
 
     # Run tb-profiler on the input reads with samplename prefix
     tb-profiler profile \
-      ${mode} \
       ${INPUT_READS} \
       --prefix ~{samplename} \
       --mapper ~{mapper} \
       --caller ~{variant_caller} \
       --calling_params "~{variant_calling_params}" \
-      --min_depth ~{min_depth} \
+      --depth ~{min_depth} \
       --af ~{min_af} \
-      --reporting_af ~{min_af_pred} \
-      --coverage_fraction_threshold ~{cov_frac_threshold} \
+      --threads ~{cpu} \
       --csv --txt \
-      $TBDB
+      ~{true="--platform nanopore" false="" ont_data} \
+      ~{additional_parameters} \
+      ${TBDB}
 
     # Collate results
     tb-profiler collate --prefix ~{samplename}
 
-    # touch optional output files because wdl
-    touch GENE_NAME LOCUS_TAG VARIANT_SUBSTITUTIONS OUTPUT_SEQ_METHOD_TYPE
-
     # merge all vcf files if multiple are present
     bcftools index ./vcf/*bcf
     bcftools index ./vcf/*gz
@@ -97,35 +87,32 @@ task tbprofiler {
       tsv_reader=csv.reader(tsv_file, delimiter="\t")
       tsv_data=list(tsv_reader)
       tsv_dict=dict(zip(tsv_data[0], tsv_data[1]))
-      with open ("MAIN_LINEAGE", 'wt') as Main_Lineage:
-        main_lin=tsv_dict['main_lineage']
-        Main_Lineage.write(main_lin)
-      with open ("SUB_LINEAGE", 'wt') as Sub_Lineage:
-        sub_lin=tsv_dict['sub_lineage']
-        Sub_Lineage.write(sub_lin)
-      with open ("DR_TYPE", 'wt') as DR_Type:
-        dr_type=tsv_dict['DR_type']
-        DR_Type.write(dr_type)
-      with open ("NUM_DR_VARIANTS", 'wt') as Num_DR_Variants:
-        num_dr_vars=tsv_dict['num_dr_variants']
-        Num_DR_Variants.write(num_dr_vars)
-      with open ("NUM_OTHER_VARIANTS", 'wt') as Num_Other_Variants:
-        num_other_vars=tsv_dict['num_other_variants']
-        Num_Other_Variants.write(num_other_vars)
-      with open ("RESISTANCE_GENES", 'wt') as Resistance_Genes:
-        res_genes_list=['rifampicin', 'isoniazid', 'pyrazinamide', 'ethambutol', 'streptomycin', 'fluoroquinolones', 'moxifloxacin', 'ofloxacin', 'levofloxacin', 'ciprofloxacin', 'aminoglycosides', 'amikacin', 'kanamycin', 'capreomycin', 'ethionamide', 'para-aminosalicylic_acid', 'cycloserine', 'linezolid', 'bedaquiline', 'clofazimine', 'delamanid']
+
+      with open ("MAIN_LINEAGE", 'wt') as main_lineage:
+        main_lineage.write(tsv_dict['main_lineage'])
+      with open ("SUB_LINEAGE", 'wt') as sublineage:
+        sublineage.write(tsv_dict['sub_lineage'])
+        
+      with open ("DR_TYPE", 'wt') as dr_type:
+        dr_type.write(tsv_dict['drtype'])
+      with open ("NUM_DR_VARIANTS", 'wt') as num_dr_variants:
+        num_dr_variants.write(tsv_dict['num_dr_variants'])
+      with open ("NUM_OTHER_VARIANTS", 'wt') as num_other_variants:
+        num_other_variants.write(tsv_dict['num_other_variants'])
+
+      with open ("RESISTANCE_GENES", 'wt') as resistance_genes:
+        res_genes_list=['rifampicin', 'isoniazid', 'ethambutol', 'pyrazinamide', 'moxifloxacin', 'levofloxacin', 'bedaquiline', 'delamanid', 'pretomanid', 'linezolid', 'streptomycin', 'amikacin', 'kanamycin', 'capreomycin', 'clofazimine', 'ethionamide', 'para-aminosalicylic_acid', 'cycloserine']
         res_genes=[]
         for i in res_genes_list:
           if tsv_dict[i] != '-':
             res_genes.append(tsv_dict[i])
         res_genes_string=';'.join(res_genes)
-        Resistance_Genes.write(res_genes_string)
-      with open ("MEDIAN_COVERAGE", 'wt') as Median_Coverage:
-        median_coverage=tsv_dict['median_coverage']
-        Median_Coverage.write(median_coverage)
-      with open ("PCT_READS_MAPPED", 'wt') as Pct_Reads_Mapped:
-        pct_reads_mapped=tsv_dict['pct_reads_mapped']
-        Pct_Reads_Mapped.write(pct_reads_mapped)
+        resistance_genes.write(res_genes_string)
+
+      with open ("MEDIAN_DEPTH", 'wt') as median_depth:
+        median_depth.write(tsv_dict['target_median_depth'])
+      with open ("PCT_READS_MAPPED", 'wt') as pct_reads_mapped:
+        pct_reads_mapped.write(tsv_dict['pct_reads_mapped'])
     CODE
   >>>
   output {
@@ -134,7 +121,7 @@ task tbprofiler {
     File tbprofiler_output_json = "./results/~{samplename}.results.json"
     File tbprofiler_output_bam = "./bam/~{samplename}.bam"
     File tbprofiler_output_bai = "./bam/~{samplename}.bam.bai"
-    File tbprofiler_output_vcf = "./vcf/~{samplename}.targets.csq.merged.vcf"
+    File? tbprofiler_output_vcf = "./vcf/~{samplename}.targets.csq.merged.vcf"
     String version = read_string("VERSION")
     String tbprofiler_main_lineage = read_string("MAIN_LINEAGE")
     String tbprofiler_sub_lineage = read_string("SUB_LINEAGE")
@@ -142,7 +129,7 @@ task tbprofiler {
     String tbprofiler_num_dr_variants = read_string("NUM_DR_VARIANTS")
     String tbprofiler_num_other_variants = read_string("NUM_OTHER_VARIANTS")
     String tbprofiler_resistance_genes = read_string("RESISTANCE_GENES")
-    Int tbprofiler_median_coverage = read_int("MEDIAN_COVERAGE")
+    Float tbprofiler_median_depth = read_float("MEDIAN_DEPTH")
     Float tbprofiler_pct_reads_mapped = read_float("PCT_READS_MAPPED")
   }
   runtime {
diff --git a/tasks/utilities/file_handling/task_cat_lanes.wdl b/tasks/utilities/file_handling/task_cat_lanes.wdl
new file mode 100644
index 000000000..60a2b7d28
--- /dev/null
+++ b/tasks/utilities/file_handling/task_cat_lanes.wdl
@@ -0,0 +1,54 @@
+version 1.0
+
+task cat_lanes {
+  input {
+    String samplename
+    
+    File read1_lane1
+    File read1_lane2
+    File? read1_lane3
+    File? read1_lane4
+
+    File? read2_lane1
+    File? read2_lane2
+    File? read2_lane3
+    File? read2_lane4
+
+    Int cpu = 2
+    Int disk_size = 50
+    String docker = "us-docker.pkg.dev/general-theiagen/theiagen/utility:1.2"
+    Int memory = 4
+  }
+  meta {
+    volatile: true
+  }
+  command <<<
+    # exit task if anything throws an error (important for proper gzip format)
+    set -euo pipefail
+    
+    exists() { [[ -f $1 ]]; }
+
+    set -euo pipefail
+
+    cat ~{read1_lane1} ~{read1_lane2} ~{read1_lane3} ~{read1_lane4} > "~{samplename}_merged_R1.fastq.gz"
+
+    if exists ~{read2_lane1} ; then
+      cat ~{read2_lane1} ~{read2_lane2} ~{read2_lane3} ~{read2_lane4} > "~{samplename}_merged_R2.fastq.gz"
+    fi
+
+    # ensure newly merged FASTQs are valid gzipped format
+    gzip -t *merged*.gz
+  >>>
+  output {
+    File read1_concatenated = "~{samplename}_merged_R1.fastq.gz"
+    File? read2_concatenated = "~{samplename}_merged_R2.fastq.gz"
+  }
+  runtime {
+    docker: "~{docker}"
+    memory: memory + " GB"
+    cpu: cpu
+    disks: "local-disk " + disk_size + " SSD"
+    disk: disk_size + " GB"
+    preemptible: 1
+  }
+}
\ No newline at end of file
diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
index 38f979119..58f0b6fb4 100644
--- a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
+++ b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
@@ -70,81 +70,6 @@
       md5sum: 3cfdda0096f0689c9829ed27bdef6b1a
     - path: miniwdl_run/call-busco/work/_miniwdl_inputs/0/test_contigs.fasta
       md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: miniwdl_run/call-busco/work/busco_downloads/file_versions.tsv
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/ancestral
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/ancestral_variants
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/dataset.cfg
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/hmms/101957at2157.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/hmms/102178at2157.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/hmms/102360at2157.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/hmms/98221at2157.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/hmms/98657at2157.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/hmms/99236at2157.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/hmms/99734at2157.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/hmms/99842at2157.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/info/ogs.id.info
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/info/species.info
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/lengths_cutoff
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/links_to_ODB10.txt
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/scores_cutoff
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/ancestral
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/ancestral_variants
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/dataset.cfg
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/hmms/1009041at2.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/hmms/1024388at2.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/hmms/1036075at2.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/hmms/1043239at2.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/hmms/961486at2.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/hmms/981870at2.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/hmms/984717at2.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/info/ogs.id.info
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/info/species.info
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/lengths_cutoff
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/links_to_ODB10.txt
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/scores_cutoff
-    - path: miniwdl_run/call-busco/work/busco_downloads/placement_files/list_of_reference_markers.bacteria_odb10.2019-12-16.txt
-    - path: miniwdl_run/call-busco/work/busco_downloads/placement_files/mapping_taxid-lineage.bacteria_odb10.2019-12-16.txt
-    - path: miniwdl_run/call-busco/work/busco_downloads/placement_files/mapping_taxids-busco_dataset_name.bacteria_odb10.2019-12-16.txt
-    - path: miniwdl_run/call-busco/work/busco_downloads/placement_files/supermatrix.aln.bacteria_odb10.2019-12-16.faa
-    - path: miniwdl_run/call-busco/work/busco_downloads/placement_files/tree.bacteria_odb10.2019-12-16.nwk
-    - path: miniwdl_run/call-busco/work/busco_downloads/placement_files/tree_metadata.bacteria_odb10.2019-12-16.txt
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/busco_sequences/fragmented_busco_sequences/108145at2157.faa
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/busco_sequences/fragmented_busco_sequences/108145at2157.fna
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/busco_sequences/single_copy_busco_sequences/84219at2157.faa
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/busco_sequences/single_copy_busco_sequences/84219at2157.fna
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/full_table.tsv
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/hmmer_output/101957at2157.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/hmmer_output/102178at2157.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/hmmer_output/102360at2157.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/hmmer_output/99734at2157.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/hmmer_output/99842at2157.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/missing_busco_list.tsv
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/short_summary.json
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/short_summary.txt
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences/1540940at2.faa
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences/1540940at2.fna
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences/1827334at2.faa
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences/1132353at2.faa
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences/1132353at2.fna
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences/1211060at2.faa
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/full_table.tsv
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/hmmer_output/1009041at2.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/hmmer_output/1024388at2.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/hmmer_output/1036075at2.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/hmmer_output/961486at2.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/hmmer_output/981870at2.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/hmmer_output/984717at2.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/missing_busco_list.tsv
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/placement_files/marker_genes.fasta
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/short_summary.json
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/short_summary.txt
-    - path: miniwdl_run/call-busco/work/test/logs/busco.log
-    - path: miniwdl_run/call-busco/work/test/logs/hmmsearch_err.log
-    - path: miniwdl_run/call-busco/work/test/logs/hmmsearch_out.log
-    - path: miniwdl_run/call-busco/work/test/logs/prodigal_err.log
-    - path: miniwdl_run/call-busco/work/test/logs/prodigal_out.log
-    - path: miniwdl_run/call-busco/work/test/logs/sepp_err.log
-    - path: miniwdl_run/call-busco/work/test/logs/sepp_out.log
     - path: miniwdl_run/call-busco/work/test/prodigal_output/predicted_genes/predicted.faa
     - path: miniwdl_run/call-busco/work/test/prodigal_output/predicted_genes/predicted.fna
     - path: miniwdl_run/call-busco/work/test/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.faa
@@ -464,7 +389,7 @@
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/_miniwdl_inputs/0/SRR2838702_R1.fastq.gz
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/_miniwdl_inputs/0/SRR2838702_R2.fastq.gz
     - path: miniwdl_run/call-read_QC_trim/call-trimmomatic_pe/command
-      md5sum: cc137a029d5143592b40edf01d53735f
+      md5sum: cc961dbda52c70200555ffb34e5ba62d
     - path: miniwdl_run/call-read_QC_trim/call-trimmomatic_pe/inputs.json
       contains: ["read", "fastq", "test", "trimmomatic_min_length"]
     - path: miniwdl_run/call-read_QC_trim/call-trimmomatic_pe/outputs.json
@@ -615,7 +540,7 @@
     - path: miniwdl_run/wdl/tasks/species_typing/escherichia_shigella/task_sonneityping.wdl
       md5sum: 3357a36f11992a0ca00c61d7bfccb44b
     - path: miniwdl_run/wdl/tasks/species_typing/mycobacterium/task_tbprofiler.wdl
-      md5sum: 3b37e6bf7f4773e12afe1fa15920acd9
+      md5sum: a4d6d24a04a453227b4fa320ff79e45f
     - path: miniwdl_run/wdl/tasks/species_typing/multi/task_ts_mlst.wdl
       md5sum: ff8070a06eca94264ad6a7d91cb03bf0
     - path: miniwdl_run/wdl/tasks/task_versioning.wdl
@@ -629,9 +554,9 @@
     - path: miniwdl_run/wdl/tasks/utilities/data_export/task_broad_terra_tools.wdl
       md5sum: 8c97c5bd65e2787239f12ef425d479ae
     - path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl
-      md5sum: d8db687487a45536d4837a540ed2a135
+      md5sum: ac49217c129add7c000eedf38acee8f3
     - path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl
-      md5sum: ea5cff6eff8c2c42046cf2eae6f16b6f
+      md5sum: f3b18a0b4c2bdeb0896176e8f9c8247d
     - path: miniwdl_run/wdl/workflows/utilities/wf_read_QC_trim_pe.wdl
       contains: ["version", "QC", "output"]
     - path: miniwdl_run/workflow.log
diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
index e12ec8ec0..06caae04d 100644
--- a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
+++ b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
@@ -70,76 +70,6 @@
       md5sum: 3cfdda0096f0689c9829ed27bdef6b1a
     - path: miniwdl_run/call-busco/work/_miniwdl_inputs/0/test_contigs.fasta
       md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: miniwdl_run/call-busco/work/busco_downloads/file_versions.tsv
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/ancestral
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/ancestral_variants
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/dataset.cfg
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/hmms/101957at2157.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/hmms/102178at2157.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/hmms/102360at2157.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/hmms/98221at2157.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/hmms/98657at2157.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/hmms/99236at2157.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/hmms/99734at2157.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/hmms/99842at2157.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/info/ogs.id.info
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/info/species.info
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/lengths_cutoff
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/links_to_ODB10.txt
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/scores_cutoff
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/ancestral
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/ancestral_variants
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/dataset.cfg
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/hmms/1009041at2.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/hmms/1024388at2.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/hmms/1036075at2.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/hmms/1043239at2.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/hmms/961486at2.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/hmms/981870at2.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/hmms/984717at2.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/info/ogs.id.info
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/info/species.info
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/lengths_cutoff
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/links_to_ODB10.txt
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/scores_cutoff
-    - path: miniwdl_run/call-busco/work/busco_downloads/placement_files/list_of_reference_markers.bacteria_odb10.2019-12-16.txt
-    - path: miniwdl_run/call-busco/work/busco_downloads/placement_files/mapping_taxid-lineage.bacteria_odb10.2019-12-16.txt
-    - path: miniwdl_run/call-busco/work/busco_downloads/placement_files/mapping_taxids-busco_dataset_name.bacteria_odb10.2019-12-16.txt
-    - path: miniwdl_run/call-busco/work/busco_downloads/placement_files/supermatrix.aln.bacteria_odb10.2019-12-16.faa
-    - path: miniwdl_run/call-busco/work/busco_downloads/placement_files/tree.bacteria_odb10.2019-12-16.nwk
-    - path: miniwdl_run/call-busco/work/busco_downloads/placement_files/tree_metadata.bacteria_odb10.2019-12-16.txt
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/full_table.tsv
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/hmmer_output/101957at2157.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/hmmer_output/102178at2157.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/hmmer_output/102360at2157.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/hmmer_output/99734at2157.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/hmmer_output/99842at2157.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/missing_busco_list.tsv
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/short_summary.json
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/short_summary.txt
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences/1540940at2.faa
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences/1540940at2.fna
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences/1132353at2.faa
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences/1132353at2.fna
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences/1505038at2.faa
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/full_table.tsv
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/hmmer_output/1009041at2.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/hmmer_output/1024388at2.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/hmmer_output/1036075at2.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/hmmer_output/961486at2.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/hmmer_output/981870at2.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/hmmer_output/984717at2.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/missing_busco_list.tsv
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/placement_files/marker_genes.fasta
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/short_summary.json
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/short_summary.txt
-    - path: miniwdl_run/call-busco/work/test/logs/busco.log
-    - path: miniwdl_run/call-busco/work/test/logs/hmmsearch_err.log
-    - path: miniwdl_run/call-busco/work/test/logs/hmmsearch_out.log
-    - path: miniwdl_run/call-busco/work/test/logs/prodigal_err.log
-    - path: miniwdl_run/call-busco/work/test/logs/prodigal_out.log
-    - path: miniwdl_run/call-busco/work/test/logs/sepp_err.log
-    - path: miniwdl_run/call-busco/work/test/logs/sepp_out.log
     - path: miniwdl_run/call-busco/work/test/prodigal_output/predicted_genes/predicted.faa
     - path: miniwdl_run/call-busco/work/test/prodigal_output/predicted_genes/predicted.fna
     - path: miniwdl_run/call-busco/work/test/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.faa
@@ -578,7 +508,7 @@
     - path: miniwdl_run/wdl/tasks/species_typing/escherichia_shigella/task_sonneityping.wdl
       md5sum: 3357a36f11992a0ca00c61d7bfccb44b
     - path: miniwdl_run/wdl/tasks/species_typing/mycobacterium/task_tbprofiler.wdl
-      md5sum: 3b37e6bf7f4773e12afe1fa15920acd9
+      md5sum: a4d6d24a04a453227b4fa320ff79e45f
     - path: miniwdl_run/wdl/tasks/species_typing/multi/task_ts_mlst.wdl
       md5sum: ff8070a06eca94264ad6a7d91cb03bf0
     - path: miniwdl_run/wdl/tasks/task_versioning.wdl
@@ -592,9 +522,9 @@
     - path: miniwdl_run/wdl/tasks/utilities/data_export/task_broad_terra_tools.wdl
       md5sum: 8c97c5bd65e2787239f12ef425d479ae
     - path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_se.wdl
-      md5sum: 4111a758490174325ae8ea52a95319e9
+      md5sum: 5e735ae6cb60f86ec7983274f3baf9f8
     - path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl
-      md5sum: ea5cff6eff8c2c42046cf2eae6f16b6f
+      md5sum: f3b18a0b4c2bdeb0896176e8f9c8247d
     - path: miniwdl_run/wdl/workflows/utilities/wf_read_QC_trim_se.wdl
       md5sum: 09d9f68b9ca8bf94b6145ff9bed2edd1
     - path: miniwdl_run/workflow.log
diff --git a/workflows/standalone_modules/wf_tbprofiler_tngs.wdl b/workflows/standalone_modules/wf_tbprofiler_tngs.wdl
index 85f75a665..2d84d91ed 100644
--- a/workflows/standalone_modules/wf_tbprofiler_tngs.wdl
+++ b/workflows/standalone_modules/wf_tbprofiler_tngs.wdl
@@ -71,7 +71,7 @@ workflow tbprofiler_tngs {
     String tbprofiler_num_dr_variants = tbprofiler.tbprofiler_num_dr_variants
     String tbprofiler_num_other_variants = tbprofiler.tbprofiler_num_other_variants
     String tbprofiler_resistance_genes = tbprofiler.tbprofiler_resistance_genes
-    Int tbprofiler_median_coverage = tbprofiler.tbprofiler_median_coverage
+    Float tbprofiler_median_depth = tbprofiler.tbprofiler_median_depth
     Float tbprofiler_pct_reads_mapped = tbprofiler.tbprofiler_pct_reads_mapped
     # tbp_parser outputs
     File tbp_parser_looker_report_csv = tbp_parser.tbp_parser_looker_report_csv
diff --git a/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl b/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl
index 32271224e..88f0ef066 100644
--- a/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl
+++ b/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl
@@ -18,6 +18,7 @@ import "../../tasks/task_versioning.wdl" as versioning
 import "../../tasks/taxon_id/contamination/task_kmerfinder.wdl" as kmerfinder_task
 import "../../tasks/taxon_id/task_gambit.wdl" as gambit_task
 import "../../tasks/utilities/data_export/task_broad_terra_tools.wdl" as terra_tools
+import "../utilities/file_handling/wf_concatenate_illumina_lanes.wdl" as concatenate_lanes_workflow
 import "../utilities/wf_merlin_magic.wdl" as merlin_magic_workflow
 import "../utilities/wf_read_QC_trim_pe.wdl" as read_qc
 
@@ -30,6 +31,15 @@ workflow theiaprok_illumina_pe {
     String seq_method = "ILLUMINA"
     File read1
     File read2
+
+    # optional additional lanes
+    File? read1_lane2
+    File? read1_lane3
+    File? read1_lane4
+    File? read2_lane2
+    File? read2_lane3
+    File? read2_lane4
+
     Int? genome_length
     # export taxon table parameters
     String? run_id
@@ -68,10 +78,24 @@ workflow theiaprok_illumina_pe {
   call versioning.version_capture {
     input:
   }
+  if (defined(read1_lane2)) {
+    call concatenate_lanes_workflow.concatenate_illumina_lanes {
+      input:
+        samplename = samplename,
+        read1_lane1 = read1,
+        read1_lane2 = select_first([read1_lane2]),
+        read1_lane3 = read1_lane3,
+        read1_lane4 = read1_lane4,
+        read2_lane1 = read2,
+        read2_lane2 = read2_lane2,
+        read2_lane3 = read2_lane3,
+        read2_lane4 = read2_lane4
+    }
+  }
   call screen.check_reads as raw_check_reads {
     input:
-      read1 = read1,
-      read2 = read2,
+      read1 = select_first([concatenate_illumina_lanes.read1_concatenated, read1]),
+      read2 = select_first([concatenate_illumina_lanes.read2_concatenated, read2]),
       min_reads = min_reads,
       min_basepairs = min_basepairs,
       min_genome_length = min_genome_length,
@@ -85,8 +109,8 @@ workflow theiaprok_illumina_pe {
     call read_qc.read_QC_trim_pe as read_QC_trim {
       input:
         samplename = samplename,
-        read1 = read1,
-        read2 = read2,
+        read1 = select_first([concatenate_illumina_lanes.read1_concatenated, read1]),
+        read2 = select_first([concatenate_illumina_lanes.read2_concatenated, read2]),
         trim_min_length = trim_min_length,
         trim_quality_min_score = trim_quality_min_score,
         trim_window_size = trim_window_size,
@@ -121,8 +145,8 @@ workflow theiaprok_illumina_pe {
       }
       call cg_pipeline.cg_pipeline as cg_pipeline_raw {
         input:
-          read1 = read1,
-          read2 = read2,
+          read1 = select_first([concatenate_illumina_lanes.read1_concatenated, read1]),
+          read2 = select_first([concatenate_illumina_lanes.read2_concatenated, read2]),
           samplename = samplename,
           genome_length = select_first([genome_length, quast.genome_length])
       }
@@ -257,8 +281,8 @@ workflow theiaprok_illumina_pe {
               sample_taxon = gambit.gambit_predicted_taxon,
               taxon_tables = taxon_tables,
               samplename = samplename,
-              read1 = read1,
-              read2 = read2,
+              read1 = select_first([concatenate_illumina_lanes.read1_concatenated, read1]),
+              read2 = select_first([concatenate_illumina_lanes.read2_concatenated, read2]),
               read1_clean = read_QC_trim.read1_clean,
               read2_clean = read_QC_trim.read2_clean,
               run_id = run_id,
@@ -608,6 +632,9 @@ workflow theiaprok_illumina_pe {
     String theiaprok_illumina_pe_analysis_date = version_capture.date
     # Read Metadata
     String seq_platform = seq_method
+    # Concatenated Illumina Reads
+    File? read1_concatenated = concatenate_illumina_lanes.read1_concatenated
+    File? read2_concatenated = concatenate_illumina_lanes.read2_concatenated
     # Sample Screening
     String read_screen_raw = raw_check_reads.read_screen
     String? read_screen_clean = clean_check_reads.read_screen
@@ -945,7 +972,7 @@ workflow theiaprok_illumina_pe {
     String? tbprofiler_sub_lineage = merlin_magic.tbprofiler_sub_lineage
     String? tbprofiler_dr_type = merlin_magic.tbprofiler_dr_type
     String? tbprofiler_resistance_genes = merlin_magic.tbprofiler_resistance_genes
-    Int? tbprofiler_median_coverage = merlin_magic.tbprofiler_median_coverage
+    Float? tbprofiler_median_depth = merlin_magic.tbprofiler_median_depth
     Float? tbprofiler_pct_reads_mapped = merlin_magic.tbprofiler_pct_reads_mapped
     String? tbp_parser_version = merlin_magic.tbp_parser_version
     String? tbp_parser_docker = merlin_magic.tbp_parser_docker
diff --git a/workflows/theiaprok/wf_theiaprok_illumina_se.wdl b/workflows/theiaprok/wf_theiaprok_illumina_se.wdl
index e743ecbce..9005766a4 100644
--- a/workflows/theiaprok/wf_theiaprok_illumina_se.wdl
+++ b/workflows/theiaprok/wf_theiaprok_illumina_se.wdl
@@ -18,6 +18,7 @@ import "../../tasks/task_versioning.wdl" as versioning
 import "../../tasks/taxon_id/contamination/task_kmerfinder.wdl" as kmerfinder_task
 import "../../tasks/taxon_id/task_gambit.wdl" as gambit_task
 import "../../tasks/utilities/data_export/task_broad_terra_tools.wdl" as terra_tools
+import "../utilities/file_handling/wf_concatenate_illumina_lanes.wdl" as concatenate_lanes_workflow
 import "../utilities/wf_merlin_magic.wdl" as merlin_magic_workflow
 import "../utilities/wf_read_QC_trim_se.wdl" as read_qc
 
@@ -29,6 +30,12 @@ workflow theiaprok_illumina_se {
     String samplename
     String seq_method = "ILLUMINA"
     File read1
+
+    # optional additional lanes
+    File? read1_lane2
+    File? read1_lane3
+    File? read1_lane4
+
     Int? genome_length
     # export taxon table parameters
     String? run_id
@@ -68,9 +75,19 @@ workflow theiaprok_illumina_se {
   call versioning.version_capture {
     input:
   }
+  if (defined(read1_lane2)) {
+    call concatenate_lanes_workflow.concatenate_illumina_lanes {
+      input:
+        samplename = samplename,
+        read1_lane1 = read1,
+        read1_lane2 = select_first([read1_lane2]),
+        read1_lane3 = read1_lane3,
+        read1_lane4 = read1_lane4
+    }
+  }
   call screen.check_reads_se as raw_check_reads { 
     input:
-      read1 = read1,
+      read1 = select_first([concatenate_illumina_lanes.read1_concatenated, read1]),
       min_reads = min_reads,
       min_basepairs = min_basepairs,
       min_genome_length = min_genome_length,
@@ -84,7 +101,7 @@ workflow theiaprok_illumina_se {
     call read_qc.read_QC_trim_se as read_QC_trim {
       input:
         samplename = samplename,
-        read1 = read1,
+        read1 = select_first([concatenate_illumina_lanes.read1_concatenated, read1]),
         trim_min_length = trim_min_length,
         trim_quality_min_score = trim_quality_min_score,
         trim_window_size = trim_window_size,
@@ -116,7 +133,7 @@ workflow theiaprok_illumina_se {
       }
       call cg_pipeline.cg_pipeline as cg_pipeline_raw {
         input:
-          read1 = read1,
+          read1 = select_first([concatenate_illumina_lanes.read1_concatenated, read1]),
           samplename = samplename,
           genome_length = select_first([genome_length, quast.genome_length])
       }
@@ -240,7 +257,7 @@ workflow theiaprok_illumina_se {
               sample_taxon = gambit.gambit_predicted_taxon,
               taxon_tables = taxon_tables,
               samplename = samplename,
-              read1 = read1,
+              read1 = select_first([concatenate_illumina_lanes.read1_concatenated, read1]),
               read1_clean = read_QC_trim.read1_clean,
               run_id = run_id,
               collection_date = collection_date,
@@ -566,6 +583,8 @@ workflow theiaprok_illumina_se {
     String theiaprok_illumina_se_analysis_date = version_capture.date
     # Read Metadata
     String seq_platform = seq_method
+    # Concatenated Illumina Reads
+    File? read1_concatenated = concatenate_illumina_lanes.read1_concatenated
     # Sample Screening
     String read_screen_raw = raw_check_reads.read_screen
     String? read_screen_clean = clean_check_reads.read_screen
diff --git a/workflows/theiaprok/wf_theiaprok_ont.wdl b/workflows/theiaprok/wf_theiaprok_ont.wdl
index a7eb9143e..867e67e0b 100644
--- a/workflows/theiaprok/wf_theiaprok_ont.wdl
+++ b/workflows/theiaprok/wf_theiaprok_ont.wdl
@@ -848,7 +848,7 @@ workflow theiaprok_ont {
     String? tbprofiler_sub_lineage = merlin_magic.tbprofiler_sub_lineage
     String? tbprofiler_dr_type = merlin_magic.tbprofiler_dr_type
     String? tbprofiler_resistance_genes = merlin_magic.tbprofiler_resistance_genes
-    Int? tbprofiler_median_coverage = merlin_magic.tbprofiler_median_coverage
+    Float? tbprofiler_median_depth = merlin_magic.tbprofiler_median_depth
     Float? tbprofiler_pct_reads_mapped = merlin_magic.tbprofiler_pct_reads_mapped
     String? tbp_parser_version = merlin_magic.tbp_parser_version
     String? tbp_parser_docker = merlin_magic.tbp_parser_docker
diff --git a/workflows/utilities/file_handling/wf_concatenate_illumina_lanes.wdl b/workflows/utilities/file_handling/wf_concatenate_illumina_lanes.wdl
new file mode 100644
index 000000000..f2a5a9ad9
--- /dev/null
+++ b/workflows/utilities/file_handling/wf_concatenate_illumina_lanes.wdl
@@ -0,0 +1,42 @@
+version 1.0
+
+import "../../../tasks/utilities/file_handling/task_cat_lanes.wdl" as concatenate_lanes
+import "../../../tasks/task_versioning.wdl" as versioning
+
+workflow concatenate_illumina_lanes {
+  input {
+    String samplename
+    
+    File read1_lane1
+    File read1_lane2
+    File? read1_lane3
+    File? read1_lane4
+    
+    File? read2_lane1
+    File? read2_lane2
+    File? read2_lane3
+    File? read2_lane4
+  }
+  call concatenate_lanes.cat_lanes {
+    input:
+      samplename = samplename,
+      read1_lane1 = read1_lane1,
+      read2_lane1 = read2_lane1,
+      read1_lane2 = read1_lane2,
+      read2_lane2 = read2_lane2,
+      read1_lane3 = read1_lane3,
+      read2_lane3 = read2_lane3,
+      read1_lane4 = read1_lane4,
+      read2_lane4 = read2_lane4
+  }
+  call versioning.version_capture {
+    input:
+  }
+  output {
+    String concatenate_illumina_lanes_version = version_capture.phb_version
+    String concatenate_illumina_lanes_analysis_date = version_capture.date
+
+    File read1_concatenated = cat_lanes.read1_concatenated
+    File? read2_concatenated = cat_lanes.read2_concatenated
+  }
+}
\ No newline at end of file
diff --git a/workflows/utilities/wf_merlin_magic.wdl b/workflows/utilities/wf_merlin_magic.wdl
index f10060851..1e19184bd 100644
--- a/workflows/utilities/wf_merlin_magic.wdl
+++ b/workflows/utilities/wf_merlin_magic.wdl
@@ -57,7 +57,7 @@ workflow merlin_magic {
     # activating tool logic
     Boolean call_poppunk = true
     Boolean call_shigeifinder_reads_input = false
-    Boolean tbprofiler_additional_outputs = false # set to true to run tbp-parser
+    Boolean call_tbp_parser = false
     # docker options
     String? abricate_abaum_docker_image
     String? abricate_vibrio_docker_image
@@ -197,14 +197,14 @@ workflow merlin_magic {
     Int srst2_gene_max_mismatch = 2000
     # tbprofiler options
     Boolean tbprofiler_run_custom_db = false
+    Boolean tbprofiler_run_cdph_db = false
     File? tbprofiler_custom_db
-    Int? tbprofiler_cov_frac_threshold
     Float? tbprofiler_min_af
-    Float? tbprofiler_min_af_pred
     Int? tbprofiler_min_depth
     String? tbprofiler_mapper
     String? tbprofiler_variant_caller
     String? tbprofiler_variant_calling_params
+    String? tbprofiler_additional_parameters
     # tbp-parser options
     String tbp_parser_output_seq_method_type = "WGS"
     String? tbp_parser_operator
@@ -215,6 +215,14 @@ workflow merlin_magic {
     File? tbp_parser_coverage_regions_bed
     Boolean? tbp_parser_debug
     Boolean? tbp_parser_add_cs_lims
+    Boolean? tbp_parser_tngs_data
+    Float? tbp_parser_rrs_frequency
+    Int? tbp_parser_rrs_read_support
+    Float? tbp_parser_rrl_frequency
+    Int? tbp_parser_rrl_read_support
+    Float? tbp_parser_rpob449_frequency
+    Float? tbp_parser_etha237_frequency
+    File? tbp_parser_expert_rule_regions_bed
     # virulencefinder options
     Float? virulencefinder_coverage_threshold
     Float? virulencefinder_identity_threshold
@@ -448,18 +456,18 @@ workflow merlin_magic {
           read2 = select_first([clockwork_decon_reads.clockwork_cleaned_read2, read2, "gs://theiagen-public-files/terra/theiaprok-files/no-read2.txt"]),
           samplename = samplename,
           ont_data = ont_data,
-          tbprofiler_run_custom_db = tbprofiler_run_custom_db,
-          tbprofiler_custom_db = tbprofiler_custom_db,
-          cov_frac_threshold = tbprofiler_cov_frac_threshold,
-          min_af = tbprofiler_min_af,
-          min_af_pred = tbprofiler_min_af_pred,
-          min_depth = tbprofiler_min_depth,
           mapper = tbprofiler_mapper,
           variant_caller = tbprofiler_variant_caller,
           variant_calling_params = tbprofiler_variant_calling_params,
+          additional_parameters = tbprofiler_additional_parameters,
+          min_depth = tbprofiler_min_depth,
+          min_af = tbprofiler_min_af,
+          tbprofiler_custom_db = tbprofiler_custom_db,
+          tbprofiler_run_custom_db = tbprofiler_run_custom_db,
+          tbprofiler_run_cdph_db = tbprofiler_run_cdph_db,
           docker = tbprofiler_docker_image
       }
-      if (tbprofiler_additional_outputs) {
+      if (call_tbp_parser) {
         call tbp_parser_task.tbp_parser {
           input:
             tbprofiler_json = tbprofiler.tbprofiler_output_json,
@@ -468,13 +476,21 @@ workflow merlin_magic {
             samplename = samplename, 
             sequencing_method = tbp_parser_output_seq_method_type,
             operator = tbp_parser_operator,
-            coverage_threshold = tbp_parser_coverage_threshold,
-            coverage_regions_bed = tbp_parser_coverage_regions_bed,
             min_depth = tbp_parser_min_depth,
             min_frequency = tbp_parser_min_frequency,
             min_read_support = tbp_parser_min_read_support,
-            tbp_parser_debug = tbp_parser_debug,
+            coverage_threshold = tbp_parser_coverage_threshold,
+            coverage_regions_bed = tbp_parser_coverage_regions_bed,
             add_cycloserine_lims = tbp_parser_add_cs_lims,
+            tbp_parser_debug = tbp_parser_debug,
+            tngs_data = tbp_parser_tngs_data,
+            rrs_frequency = tbp_parser_rrs_frequency,
+            rrs_read_support = tbp_parser_rrs_read_support,
+            rrl_frequency = tbp_parser_rrl_frequency,
+            rrl_read_support = tbp_parser_rrl_read_support,
+            rpob449_frequency = tbp_parser_rpob449_frequency,
+            etha237_frequency = tbp_parser_etha237_frequency,
+            expert_rule_regions_bed = tbp_parser_expert_rule_regions_bed,
             docker = tbp_parser_docker_image
         }
       }
@@ -896,7 +912,7 @@ workflow merlin_magic {
     String? tbprofiler_sub_lineage = tbprofiler.tbprofiler_sub_lineage
     String? tbprofiler_dr_type = tbprofiler.tbprofiler_dr_type
     String? tbprofiler_resistance_genes = tbprofiler.tbprofiler_resistance_genes
-    Int? tbprofiler_median_coverage = tbprofiler.tbprofiler_median_coverage
+    Float? tbprofiler_median_depth = tbprofiler.tbprofiler_median_depth
     Float? tbprofiler_pct_reads_mapped = tbprofiler.tbprofiler_pct_reads_mapped
     String? tbp_parser_version = tbp_parser.tbp_parser_version
     String? tbp_parser_docker = tbp_parser.tbp_parser_docker