v1.4.2

Hotfix to add support for Pangolin v3.0+ output format changes for assigning lineages and postprocessing.

v1.4.1

Hotfix to add support for Pangolin v2.4 output format changes when assigning lineages.

v1.4.0

• Add quick alignment of iVar and FreeBayes consensus sequences if FreeBayes is run
• Updates to postprocessing reports including the addition of Pangolin lineage assignments and consensus nucleotide differences between iVar and FreeBayes
• Individual sample and summary reports are more dynamic, only displaying information generated by optional tools if run through SIGNAL and output files found
• SIGNAL ncov_tools now takes a list of negative control sample identifiers or prefixes to provide a more complete ncov-tools config.yaml file
• Fixed a dependancy issue when running BreSeq through SIGNAL

v1.3.0

• Add FreeBayes consensus and variant calling in parallel with iVar (option can be activated in config file along with BreSeq)
• Updates to SIGNAL postprocess to indicate differences in variant calls between iVar and FreeBayes
• Restore multiple pool samples support (now only applies to samples sharing the same sample identifier in the sample table)
• Updated sample table generator script (generate_sample_table.sh) to handle FASTQ files for multiple pool samples
• Updates to ncov-tools submodule (automatically formats data for ncov-tools v1.4+, but manual run of ncov-tools is still required)
• Updated README

v1.2.1

Hotfix to add missing parenthesis in human host filtering script when no reads remain

v1.2.0

• Update kraken2 to handle changes to NCBI taxonomy
• Add lineage assignment script for nextclade and pangolin (includes autoupdate of these tools on running)
• Updated README

v1.1.0

• Removes multiple pool samples support (as this isn't used, was fragile, and introduced bugs)
• Update to ivar 1.3
• Makes running breseq optional
• Updates ncov-tools submodule (automatically formats data for ncov-tools manual run but automatic running of this still has issues related to nested conda envs).

v1.0.0

Start of formal workflow semantic versioning.

This version includes competitive host removal using a composite reference and interactive summary report generation.

Note: earlier releases do not follow semvar but it will be used from this point onwards.

v0.9.0

Last commit using prior host removal strategy (i.e. removing any reads that maps against human reference with >30 BWA dynamic score alignment (not MAPQ as erroneously stated)).

v0.1.0

Final version of the initial workflow (i.e. before adoption of the "consensus core" set of tools using bwa+ivar).