Version 2.2.0

2.2.0 - 2024/09/26

Added

• Added the ability to include a sample_name column in the input samplesheet.csv. Allows for compatibility with IRIDA-Next input configuration PR24
  • sample_name special characters will be replaced with "_"
  • If no sample_name is supplied in the column sample will be used
  • To avoid repeat values for sample_name all sample_name values will be suffixed with the unique sample value from the input file

2.1.1

2.1.1 - 2024/05/02

Changed

• Enabled checking for existence of database files in JSON Schema to avoid issues with staging non-existent files in Azure.

2.1.0

2.1.0 - 2024/05/01

Added

• The ability to handle errors that occur during quality trimming, alignment to selected database, and taxon abundance estimation. These errors will be reported in failure/failures_report.csv.

Changed

• Refined the calculations within the 'adjust_bracken_for_unclassified_reads' function to ascertain the proportions of taxonomic abundances relative to the read values adjusted following Bracken's re-estimation of abundances.

2.0.0

2.0.0 - 2024/04/18

Added

• The initial release of phac-nml/speciesabundance as a Nextflow pipeline following nf-core standards.

Changed

• Migrated SpeciesAbundance to a Nextflow pipeline.
• Updated the SpeciesAbundance release version from 1 to 2 to reflect migration from the Galaxy-based pipeline.