Skip to content

Commit

Permalink
update version tag (#622)
Browse files Browse the repository at this point in the history
  • Loading branch information
@sage-wright
sage-wright authored Sep 17, 2024
1 parent dab1316 commit 9a10de7
Show file tree
Hide file tree
Showing 6 changed files with 6 additions and 6 deletions.
2 changes: 1 addition & 1 deletion docs/index.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,7 @@ When undertaking genomic analysis using the command-line, via Terra, or other da
We continuously work to improve our codebase and usability of our workflows by the public health community, so changes from version to version are expected. This documentation page reflects the state of the workflow at the version stated in the title.

!!! dna "What's new?"
You can see the changes since PHB v2.1.0 [**here**](https://theiagen.notion.site/Public-Health-Bioinformatics-v2-2-0-Minor-Release-Notes-9b2781f27b8d4b69949f8fc1ef04868d?pvs=4)!
You can see the changes since PHB v2.2.0 [**here**](https://theiagen.notion.site/Public-Health-Bioinformatics-v2-2-1-Patch-Release-Notes-104cb013bc9380bcbd70dab04bf671a8?pvs=74)!

## Contributing to the PHB Repository

Expand Down
2 changes: 1 addition & 1 deletion docs/workflows/phylogenetic_construction/snippy_variants.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,7 @@ The `Snippy_Variants` workflow aligns single-end or paired-end reads (in FASTQ f

### Outputs

!!! tip "Visualize your outputs in IGB"
!!! tip "Visualize your outputs in IGV"
Output bam/bai files may be visualized using IGV to manually assess read placement and SNP support.

| **Variable** | **Type** | **Description** |
Expand Down
2 changes: 1 addition & 1 deletion docs/workflows_overview/workflows_alphabetically.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ title: Alphabetical Workflows
| [**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) |
| [**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) |
| [**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) |
Expand Down
2 changes: 1 addition & 1 deletion docs/workflows_overview/workflows_kingdom.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ title: Workflows by Kingdom
| [**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) |
| [**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) |
| [**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) |
Expand Down
2 changes: 1 addition & 1 deletion docs/workflows_overview/workflows_type.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -74,7 +74,7 @@ title: Workflows by Type
| [**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) |
| [**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) |
| [**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) |
Expand Down
2 changes: 1 addition & 1 deletion tasks/task_versioning.wdl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ task version_capture {
volatile: true
}
command {
PHB_Version="PHB v2.2.0"
PHB_Version="PHB v2.2.1"
~{default='' 'export TZ=' + timezone}
date +"%Y-%m-%d" > TODAY
echo "$PHB_Version" > PHB_VERSION
Expand Down

0 comments on commit 9a10de7

Please sign in to comment.