taxtriage - 2.1.1

What's Changed

• Single Sample addition as input
• Downsampling (changed from khmer) with BBNorm by @Merritt-Brian in https://github.com/jhuapl-bio/taxtriage/pull/97
• Remote some unused parameters for tower
• Adding single sample input (one sample only) - This method overwrites the --input if specified.
• Updates to usage for the above.

Full Changelog: https://github.com/jhuapl-bio/taxtriage/compare/v2.1.0...v2.1.1

- Python
Published by Merritt-Brian 11 months ago

taxtriage - 2.1.0

What's Changed

• Annotation and CDS Mappings by @Merritt-Brian in https://github.com/jhuapl-bio/taxtriage/pull/96

• Added CDS mapping back into V2.0

• Fixed Reference assembly

• Updated to allow Genbank as a potential resource

• Added Alternative Name matching for pathogen sheet

• Added several versions into MultiQC report at the end

Full Changelog: https://github.com/jhuapl-bio/taxtriage/compare/v2.0.7...v2.1.0

- Python
Published by Merritt-Brian 11 months ago

taxtriage - 2.0.8

Hotfix Path:

Host removal of reads was not properly being used due to the global minmapq variable. Default to empty value for minmapq for the host removal step

- Python
Published by Merritt-Brian about 1 year ago

taxtriage - 2.0.7

• Added confidence metric merging of region fix for gap acceptance (0-depth)
• Updated Pathogen Sheet with new annotations
• Added High Consequence Column to report/html of MultiQC
• Update README with new parameter
• Added High Consequence Table for low TASS scores to bottom of report
• Update configurations for RAM needed for score calculations

- Python
Published by Merritt-Brian about 1 year ago

taxtriage - 2.0.6

• Use fasta file(s) as regional comparisons for sourmash during alignment confidence
• Update to the workflow diagram

- Python
Published by Merritt-Brian about 1 year ago

taxtriage - 2.0.5

Hotfix for singularity users where the incorrect url was being given for the alignment confidence metric step

- Python
Published by Merritt-Brian about 1 year ago

taxtriage - 2.0.4

• Fix to include reference to correct container on quay for calculating alignment score
• Update to pathogen name mapping (again)
• MultiQC formatting changes
• Change alignment scoring to suphigh config (for now)

- Python
Published by Merritt-Brian about 1 year ago

taxtriage - v2.0.3

What's Changed

• Fixmtchpatchs by @Merritt-Brian in https://github.com/jhuapl-bio/taxtriage/pull/84

Full Changelog: https://github.com/jhuapl-bio/taxtriage/compare/v2.0.2...v2.0.3

- Python
Published by Merritt-Brian about 1 year ago

taxtriage - 2.0.2

• Adding throughput increase for Sourmash scaling needs
• Updated Pathogens FASTA to include herpesvirus 3
• Introduced dispersion factors for gini calculations

- Python
Published by Merritt-Brian about 1 year ago

taxtriage - 2.0.1

Hotfix for cpu worker definition causing cloud issues

- Python
Published by Merritt-Brian about 1 year ago

taxtriage - 2.0.0

Version 2 update for confidence metrics

- Python
Published by Merritt-Brian about 1 year ago

taxtriage - 1.7.0

• Updates to MCE configurations for version 1 of the confidence metric
• Updating weight options to adjust defaults for final TASS Score
• Allow ignore weights if DIAMOND or K2 fail or skipped in final tass score

- Python
Published by Merritt-Brian about 1 year ago

taxtriage - 1.6.0

• Sets Minimap2 to a default aligner for short reads
• Adds K2 to the Organism Discovery Report

- Python
Published by Merritt-Brian over 1 year ago

taxtriage - 1.5.0

• Additions to the pathogen annotation sheet
• Merging of redundant pathogen strains/subsp in final report
• Improvements in confidence metric reporting
• Additional Databases (default) added

- Python
Published by Merritt-Brian almost 2 years ago

taxtriage - 1.4.1

1. Added fix for improper assembly prioritization
2. Changed de-novo assembly to Megahit
3. Properly give distribution metrics in report

- Python
Published by Merritt-Brian almost 2 years ago

taxtriage - 1.4.0

- Python
Published by Merritt-Brian almost 2 years ago

taxtriage - 1.3.3

Bug Fixes: - Fixed a routing and mismatch of Reads and Pulled reference FASTA file during alignment (Pulled assembles only) Example Reads For Sample A pull Reference A and Sample B Reads pull Reference B but Sample A aligns to Reference B and Sample B aligns to Reference A - Multi-sample runs were not reporting full list to the metagenomics discovery report

- Python
Published by Merritt-Brian about 2 years ago

taxtriage - 1.3.2

• Fixed an issue with NF Tower not produced krona plots
• Made "pathogen report" mandatory - defaults to the one in assets/pathogen_sheet.txt
• Updated nf tower configurations
• Changed the "organisms" parameter to produce a file first to avoid pathing issues for cloud

- Python
Published by Merritt-Brian about 2 years ago

taxtriage - 1.3.1

• Fixed an error with empty confidence merging
• indexing repeats no longer happen for merged report on a multi-sample run
• Force exit (with text) if skip kraken2 called AND no organism list or reference fasta provided

- Python
Published by Merritt-Brian about 2 years ago

taxtriage - 1.3.0

Features

• Fuzzy matching option (taxid vs name of organism)
• Turn off de novo assembly and variant analysis by default. Requires parameters to enable
• Allow GCF mapping to existing NC accessions if not present. Requires refseq conventions
• Skippable Kraken2 - goes into alignment post QC/trimming
• Merged Confidence Metrics into a per sample x organism basis in the report

- Python
Published by Merritt-Brian about 2 years ago

taxtriage - 1.2.2

- Python
Published by Merritt-Brian over 2 years ago

taxtriage - 1.2.1

- Python
Published by Merritt-Brian over 2 years ago

taxtriage - 1.2.0

- Python
Published by Merritt-Brian over 2 years ago

taxtriage - 1.1.0

- Python
Published by Merritt-Brian over 2 years ago

taxtriage - 1.0.1

Setting first stable release v1.0.1

- Python
Published by Merritt-Brian over 2 years ago

taxtriage - 1.0.0

Initial (v1.0.0) release of TaxTriage

- Python
Published by Merritt-Brian over 3 years ago