v1.6.7

• Hotfixes for SIGNAL postprocess and ncov_tools
• For postprocess: fix TypeError upon generating HTML output where missing files produce unconverted NoneType values when strings are expected
• For ncov_tools: fix pathing that resulted in the ncov-tools-results directory containing duplicate files

v1.6.6

• Hotfix for signalexe.py ncov_tools where ncov-tools would fail to execute if the SIGNAL results directory was not found in the root of the repository
• Results can now be at differing depths within the filesystem so long as the path (absolute or relative) is defined within the SIGNAL config.yaml

v1.6.5

• Hotfix to SIGNAL postprocess circumventing a WorkflowError due to BreSeq providing an invalid or empty index.html
• Both instances will be treated the same, with no information extracted and an empty column in its place

v1.6.4

• Patch to fix Pangolin version updating when starting with a current local installation of pangolin v3.1.11 or below where the --all-versions flag did not exist. This prevents such error from exiting the entire pipeline and allowing for the software to be updated
• Modified output when software versions do not match when assessing lineage output as opposed to exiting the program with an error outright
• Added Breseq parameters for minor variant thresholds to be defined by the user
• Defaults are set automatically for added Breseq parameters (see below), if not found in existing (i.e., previous versions of) config.yaml files

Updates to config.yaml:

# Used as --polymorphism-minimum-variant-coverage-each-strand, --polymorphism-frequency-cutoff arguments
# Parameters needed to determine thresholds for minor variant detection
polymorphism_variant_coverage: 2
polymorphism_frequency: 0.05

v1.6.3

Added support for Nextclade v3+ and associated datasets:

• Updated lineage assignment rules within SIGNAL all for Nextclade v3+ support
• Backwards compatibility maintained between v3 and v2 in both software and datasets where both can be specified via the yaml configuration file
• Includes fix where Nextclade version, when specified, would not update as requested
• Nextclade dataset tag will now be properly identified when reporting final versions of software and datasets, if not specified by the user
• Updated general format of the yaml configuration file for clarity on Nextclade parameters (reflected when using signalexe.py --config-only). Parameters remain unchanged. See below:

# Versions for Nextclade (software & datasets)
# nextclade: Software version. Input should use numbers only (i.e., 2.14.0)
# nextclade-data: The nextclade dataset tag. Refer to available nextclade datasets. Accepted tag format is 'YYYY-mm-ddTHH:MM:SSZ'
# Be as specific as possible with the desired dataset tag. Can accept dates (YYYY-mm-dd) alone, but will assume corresponding timestamp (HH:MM:SS). SIGNAL will automatically adjust between v2 and v3 dataset tag formats
# Leave blank for latest versions
nextclade:
nextclade-data:

# Nextclade v2 only
# nextclade-include-recomb: set to False will download the recombinant-sequence free version of the nextclade dataset
nextclade-include-recomb: True

General updates:

• General performance update allowing mamba to be used when updating lineage assignment software
• Updated dependencies for SIGNAL postprocess

v1.6.2

• Important hotfix to address software version incompatibility for rules using the snp_mapping environment
• Minor tweak to address x-axis label clipping in generated coverage plots

v1.6.1

• Hotfix aims to improve the linking between iVar and Freebayes consensus and variant output when using ncov_tools to reduce errors
• Minor tweaks to handle missing or erroneous output mid-analysis due to errors

v1.6.0

Major updates to SIGNAL execution:

• signal.py has been renamed to signalexe.py
• signalexe.py install option allows for per-rule environment installation without requiring input data (future versions will include testing using curated data)
• --data flag added to allow you to specify the location of file data dependencies
• Additional snakemake parameters have been added as options for signalexe.py including: --ignore-incomplete and --quiet

General updates:

• Improved handling of failed samples that would otherwise produce snakemake errors. Samples that fail assembly will be logged within a new output file: failed_samples.log, found within the results directory
• Improved linking of prerequisite files for ncov-tools (when executing signalexe.py ncov_tools) where failed samples will be excluded to minimize errors
• Nextclade dataset download now skippable if provided version (within configuration file) matches one already found within scripts/nextclade. This also makes the lineage assignment portion of SIGNAL more offline-friendly as SIGNAL will use whichever datasets are available within scripts/nextclade if it cannot update. This updating now follows the same logic as Pangolin and Nextclade updating
• Updates to per-rule conda environments to remove stale packages

Additional (optional) scripts:

• General extraction script (scripts/get_signal_results.sh) provided which can be used to pull consensus, variant, and select reports from SIGNAL + ncov-tools

v1.5.9

• Important hotfix to maintain dependencies for Pangolin

v1.5.8

• Minor tweak for Nextclade software updating
• Quality of life updates, namely the incorporation of select snakemake parameters into the signal.py executable
• Added flags: --rerun-incomplete, --forceall, --dry-run, --unlock, and --verbose