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

1.6.0

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

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

1.4.1

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

1.4.0

v1.4.0

Set v1.4.0 tag release

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

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

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

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

1.2.2

Merge pull request #38 from jhuapl-bio/main

allow clean fastq.gz