The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
- Added the ability to include a
sample_namecolumn in the input samplesheet.csv. Allows for compatibility with IRIDA-Next input configuration PR24sample_namespecial characters will be replaced with"_"- If no
sample_nameis supplied in the column sample will be used - To avoid repeat values for
sample_nameallsample_namevalues will be suffixed with the uniquesamplevalue from the input file
- Enabled checking for existence of database files in JSON Schema to avoid issues with staging non-existent files in Azure.
- 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.
- 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.
- The initial release of phac-nml/speciesabundance as a Nextflow pipeline following nf-core standards.
- This pipeline will estimate the relative abundance of sequence reads originating from different species in a sample from Illumina short-read data.
- Migrated SpeciesAbundance to a Nextflow pipeline, with integration testing using nf-test.
- Updated the SpeciesAbundance release version from 1 to 2 to reflect migration from the Galaxy-based pipeline.