Version 2.0.1

What's Changed

• Bugfix: int string comparison for nextclade

Full Changelog: 2.0.0...2.0.1

Version 2.0.0

v2.0.0 - [2024-04-30]

Overall version 2.0.0 has the all the same outputs as version 1.1.0 but with some adjustments to the output locations and the input parameter names. This makes this release incompatible with previous automation unfortunately but it is ultimately for a more robust and easier to run/develop pipeline

Added

• Nextclade for an additional validation to frameshifts
  • Run nextclade with specified args to create TSV output
    • The TSV output is used to help validate frameshifts by looking at the consensus sequence and determining if there are any frameshifts and if they are known. Known frameshifts can be used to help correct the qc_pass column
  • Nextclade specific args added:
    • --nextclade_dataset: Name of nextclade dataset to pull. Default: 'sars-cov-2'
    • --nextclade_tag: Tag of nextclade dataset to pull. Default: '2024-04-15--15-08-22Z'
• New Params
  • Max resource args for some customizable resource management
  • local_scheme arg to make it easier to provide a local primer scheme
  • --no_longshot arg to allow skipping longshot in artic medaka pipeline
• Scheme validation workflow
  • Checks that the folders are found with the needed files
  • Creates amplicon bed file for ncov-tools
  • Detects primer names

Changed

• Input param arguments
  • No longer both snake_case and camelCase args
  • All args have been set to snake_case
    • --medakaModel to --medaka_model
    • --schemeRepoURL to --scheme_repo_url
    • --schemeVersion to --scheme_version
    • --minReadsPerBarcode to --min_reads_per_barcode
    • --minReadsGuppyPlex to --min_reads_guppyplex
    • --correctN to --skip_correct_n and logic changes
    • --sequencingTechnology to --sequencing_technology
    • --csqAfThreshold to --csq_af_threshold
    • --csqDpThreshold to --csq_dp_threshold
• Output file locations
  • Output locations are still based on the process name. These have been deduplicated to make development and updates easier leading to a slight difference.
    • articNcovNanopore_sequenceAnalysisMedaka_articDownloadScheme to articNcovNanopore_schemeValidate_validateScheme/
    • articNcovNanopore_sequenceAnalysisMedaka_articGuppyPlex to articNcovNanopore_articGuppyPlex
    • articNcovNanopore_sequenceAnalysisNanopolish_articMinIONNanopolish to articNcovNanopore_articMinION
    • articNcovNanopore_sequenceAnalysisMedaka_articMinIONMedaka to articNcovNanopore_articMinION
    • articNcovNanopore_sequenceAnalysisMedaka_renameSamples to articNcovNanopore_renameBarcodeSamples
• Nextflow config utilization
  • Removed params from the base.config config and placed them in the main nextflow.config
  • base.config now for resource setting
• Ncov-tools config
  • Cleaned up ncov-tools config comments
  • Allow run name and primer names to be set by pipeline instead of being locked in by config

Removed

• All Illumina steps and args
• All climb upload steps and args
• --schemeDir parameter
  • Now scheme directory is automatically adjusted to primer-schemes

Developer Changes

• Test dataset fastq files were gzipped to save more space
• Tests that were not being run were removed
• Formatting/organization of nextflow workflow code was revisited and standardized
• Formatting/organization of most python code was revisited
• Removal of duplication of workflows and modules
  • Ex. articMinionNanopolish module and articMinionMedaka module consolidated to one articMinion module
  • Individual workflows for --nanopolish and --medaka were combined into one workflow as the steps were almost all the same
• Better passing of variables/channels to processes
• Updated channel creation and handling of empty channels