bump version and update docs

docs/workflows/genomic_characterization/theiaprok.md

@@ -417,7 +417,7 @@ All input reads are processed through "[core tasks](#core-tasks-performed-for-al
 | 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_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:1.6.0 | 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 |
@@ -432,8 +432,6 @@ All input reads are processed through "[core tasks](#core-tasks-performed-for-al
 | 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 | **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 | **tbprofiler_additional_parameters** | String | Add additional parameters to the tbprofiler command |  | 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 |

docs/workflows_overview/workflows_alphabetically.md

@@ -11,10 +11,11 @@ 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) |

docs/workflows_overview/workflows_kingdom.md

@@ -15,6 +15,7 @@ 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) |
 | [**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) |
@@ -75,7 +76,7 @@ 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) |
 | [**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) |