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Recent Releases of covid-19-signal

covid-19-signal - 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

- Python
Published by jaleezyy almost 2 years ago

covid-19-signal - 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

- Python
Published by jaleezyy almost 2 years ago

covid-19-signal - 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

- Python
Published by jaleezyy almost 2 years ago

covid-19-signal - 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

polymorphismvariantcoverage: 2 polymorphism_frequency: 0.05 ```

- Python
Published by jaleezyy almost 2 years ago

covid-19-signal - 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

- Python
Published by jaleezyy over 2 years ago

covid-19-signal - 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

- Python
Published by jaleezyy about 3 years ago

covid-19-signal - 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

- Python
Published by jaleezyy about 3 years ago

covid-19-signal - 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

- Python
Published by jaleezyy about 3 years ago

covid-19-signal - v1.5.9

  • Important hotfix to maintain dependencies for Pangolin

- Python
Published by jaleezyy about 3 years ago

covid-19-signal - 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

- Python
Published by jaleezyy over 3 years ago

covid-19-signal - v1.5.7

  • Important hotfix fixing errors when generating or updating conda environments for lineage assignment via SIGNAL all
  • Updated ncov-tools submodule to v1.9.1
  • Updated SIGNAL ncov_tools to incorporate pangolin option --analysis-mode when producing the configuration file

- Python
Published by jaleezyy over 3 years ago

covid-19-signal - v1.5.6

  • Hotfix to lineage assignment (part of SIGNAL all) for Nextclade v2+ support
  • Version specification possible within the configuration file so Nextclade v1 support remains
  • Configuration files (and examples) along with signal.py have been updated:

```

Versions for Nextclade (software & datasets)

Software version (nextclade) should use numbers only (i.e., 1.11.0)

Be as specific as possible with the desired dataset tag (nextclade-data). Can accept dates (YYYY-mm-dd) alone, but will assume corresponding timestamp (HH:MM:SS)

Typical tag format is YYYY-mm-ddTHH:MM:SSZ

Leave blank for latest versions

Setting nextclade-include-recomb to False will download the recombinant-sequence free version of the Nextclade database

nextclade: nextclade-data: nextclade-include-recomb: True ```

  • ncov-tools submodule link has been updated

- Python
Published by jaleezyy almost 4 years ago

covid-19-signal - v1.5.5

  • Added support for ncov-tools v1.9.0 and continued support for the latest version(s) of Pangolin
  • Corrections made to lineage calling output (from SIGNAL all) to ensure version compatibility across lineage calling tools

- Python
Published by jaleezyy about 4 years ago

covid-19-signal - v1.5.4

  • Hotfix to correct missing columns in lineage assignment TSV output, namely columns missing for Pangolin QC and version(s).

- Python
Published by jaleezyy about 4 years ago

covid-19-signal - v1.5.3

Dependency update:

  • Nextclade updated now through conda (replacing depreciated Node.js version)
  • SIGNAL all output adjusted to newer nextclade versions; SIGNAL postprocess summary output remains unchanged

Parameter updates:

  • New parameters (nextclade-data and nextclade-include-recomb) allow for version selection for nextclade datasets (tags for both sars-cov-2 and sars-cov-2-no-recomb datasets supported). Latest sars-cov-2 dataset is the default download.
  • New parameter (pangolin_fast) allows for for the alternate pangolin --analysis-mode fast to be executed, using Pangolearn in place of Usher. Default is False to remain using Usher.

General update:

  • Performance update to version-specific installation of lineage calling software whereby the pangolin version will dictate what other dependencies subsequently update

Configuration file additions are as followed:

```

Toggle faster Pangolin analysis at the cost of accuracy (uses Pangolearn instead of Usher)

Use for significantly larger datasets

pangolin_fast: False

Required for Nextclade (datasets)

Be as specific as possible with the desired tag. Can accept dates (YYYY-mm-dd) alone, but will assume corresponding timestamp (HH:MM:SS)

Typical tag format is YYYY-mm-ddTHH:MM:SSZ

Leave blank for latest dataset

Setting nextclade-include-recomb to False will download the recombinant-sequence free version of the Nextclade database

nextclade-data: nextclade-include-recomb: True ```

- Python
Published by jaleezyy about 4 years ago

covid-19-signal - v1.5.2

  • Hotfix to fix pangoLEARN updating where it always pulled the latest release regardless of what was specified in the configuration file.

- Python
Published by jaleezyy about 4 years ago

covid-19-signal - v1.5.1

Hotfix to lineage assignment (part of SIGNAL all) and postprocessing (i.e., SIGNAL postprocess) for Pangolin v4.0+ support: - Version control of lineage assignment software (i.e., Pangolin) retains support for older dependencies (pangoLEARN and pango-designation), while updating the new required ones (new parameter: pangolin-data) if the latest version(s) are used. All will update accordingly - Configuration files (and examples) have been updated ```

Versions of software related to lineage calling (use numbers only, i.e., 3.1.1). Dates are accepted for pangolearn. Leave blank for latest version(s).

pangolin: constellations: scorpio:

Required for Pangolin <v4.0

pangolearn: pango-designation:

Required for Pangolin v4+

pangolin-data: ``` - Postprocessing will adjust for the output format changes in Pangolin

- Python
Published by jaleezyy about 4 years ago

covid-19-signal - v1.5.0

  • Patches to handle empty FASTQs after trimming/filtering
  • Versions for lineage assignment tools (i.e., Pangolin) to be used in SIGNAL can now be specified in the configuration file: # Use numbers only, i.e., 3.1.1). Dates are accepted for pangolearn. Leave blank for latest version(s). pangolin: pangolearn: constellations: scorpio: pango-designation:
  • Quality of life improvements, namely a SIGNAL executable entry script (i.e., signal.py) to ease overall use
  • ncov-tools submodule has been integrated and will run after initial filesystem setup when executing SIGNAL ncov_tools with FreeBayes consensus and variant files to be prioritized, if FreeBayes was run (i.e., run_freebayes: True) and corresponding files are found within the results directory.
  • Updates to README with more specific instructions

- Python
Published by jaleezyy over 4 years ago

covid-19-signal - v1.4.4

  • Hotfix to update lineage assessment conda environment (fixes support for Pangolin v3.1.12+)
  • Removed NextStrain clade assertion and corrected reporting to compare iVar and FreeBayes
  • Sample table generating script updated to support more generic naming

- Python
Published by jaleezyy over 4 years ago

covid-19-signal - v1.4.3

  • Hotfix to add required conda environment changes for Pangolin v3.1+ when assigning lineages
  • Minor parameter update to ncov-tools config.yaml generation via SIGNAL ncov_tools

- Python
Published by jaleezyy almost 5 years ago

covid-19-signal - v1.4.2

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

- Python
Published by jaleezyy about 5 years ago

covid-19-signal - v1.4.1

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

- Python
Published by jaleezyy about 5 years ago

covid-19-signal - 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

- Python
Published by jaleezyy about 5 years ago

covid-19-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

- Python
Published by jaleezyy about 5 years ago

covid-19-signal - v1.2.1

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

- Python
Published by fmaguire over 5 years ago

covid-19-signal - 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

- Python
Published by fmaguire over 5 years ago

covid-19-signal - 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).

- Python
Published by fmaguire over 5 years ago

covid-19-signal - v0.1.0

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

- Python
Published by fmaguire almost 6 years ago

covid-19-signal - 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)).

- Python
Published by fmaguire almost 6 years ago

covid-19-signal - 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.

- Python
Published by fmaguire almost 6 years ago