Skip to content

CHANGELOG.md

Latest commit

 

History

History
143 lines (109 loc) · 7.02 KB

CHANGELOG.md

File metadata and controls

143 lines (109 loc) · 7.02 KB

bactopia/nf-bactopia: Changelog

v2.0.1

Fixed

  • Ensured meta is always a nextflow.util.RecordMap so downstream Nextflow processes receive a proper Record type instead of a plain Map:
    • collectBactopiaInputs(), processFOFN(), processAccession(), and processAccessions() in Bactopia.groovy now wrap meta in RecordMap on every runtype return path (paired-end, single-end, hybrid, short_polish, assembly, ont, merge-pe, merge-se)
    • _collectInputs() in BactopiaTools.groovy promotes inputs['meta'] to RecordMap before returning
    • gather() / _gather() and gatherFields() in ChannelUtils.groovy promote meta via a new idempotent _asRecordMap() helper in both channel and list code paths

v2.0.0

Added

  • New channel functions for record-based workflows:
    • gatherCsvtk() - gather a single field and rename to csv for CSVTK_CONCAT input
    • gatherFields() - gather multiple fields with explicit rename mapping
    • collectNextflowLogs() - expand record nf_logs into [meta, file] tuples for publishing
    • combineWith() - cartesian product combining gathered channels with multi-item channels (replaces deprecated Nextflow each input qualifier)

Changed

  • Breaking: Bumped minimum Nextflow version to 26.03.1-edge
  • Breaking: gather() now returns record-like maps instead of [meta, outputSet] tuples
    • New signature: gather(Object chResults, String field, Map meta)
    • field is now a required positional parameter specifying the record field to extract
    • meta is a required Map that passes through as-is to output (must contain name)
    • Output meta key changed from id to name
    • Removed deprecated tuple mode entirely
  • Breaking: Removed flattenPaths() function (replaced by gatherFields() and combineWith())
  • Breaking: Removed empty file placeholders — input maps now use empty lists ([]) instead of EMPTY_PATHS sentinel files
    • collectBactopiaInputs(), processFOFN(), processAccessions(), processAccession() no longer require empty_path parameter
    • _collectInputs() in BactopiaTools no longer requires EMPTY_PATHS parameter
  • Updated input return types from indexed tuples to named Maps for record type compatibility
    • collectBactopiaInputs(), processFOFN(), processAccessions(), processAccession() now return Maps with named keys (meta, r1, r2, se, lr, assembly)
  • Refactored gather() internals to use a private _gather() method with field mapping support

Fixed

  • Fixed BactopiaSchema.cleanParameters() converting LinkedHashMap values to String instead of recursively cleaning them as nested Maps
  • Fixed .endsWith() calls on database path parameters (bakta_db, eggnog_db, gtdb, kraken2_db) to use .toString() to handle non-String types
  • Fixed all tests to align with record type refactor and empty file removal

v1.0.9

Added

  • Added channel manipulation functions: gather(), flattenPaths(), and formatSamples()
  • Added utility classes: ChannelUtils and SampleUtils for cleaner code organization
  • Added 230 comprehensive unit tests achieving 61.6% instruction coverage:
    • Core Plugin Components:
      • BactopiaExtension (30 tests) - all @Function methods
      • BactopiaFactory (1 test) - plugin initialization
      • BactopiaObserver (8 tests) - lifecycle and event handling
    • Validation & Utilities:
      • BactopiaUtils (26 tests) - file validation, parameter utilities
      • BactopiaUtilsParameter (10 tests) - parameter summary functions
    • Input Processing:
      • BactopiaTools inputs (26 tests) - tool input collection
      • Bactopia inputs (22 tests) - workflow input collection
      • Sample utilities (26 tests) - sample formatting, validation, and DataflowVariable support
      • Channel utilities (20 tests) - channel operations, validation, and DataflowQueue support
    • Schema & Validation:
      • BactopiaSchema (17 tests) - parameter cleaning and type conversions
    • Templates & Output:
      • BactopiaTemplate (7 tests) - utility functions (getLogColors, dashedLine)
      • BactopiaTemplateRendering (12 tests) - logo rendering for 12 workflows
      • BactopiaMotD (4 tests) - Message of the Day generation
    • Configuration:
      • BactopiaConfig (7 tests) - configuration management
      • BactopiaLoggerFactory (14 tests) - logging capture and management
  • Added JaCoCo coverage reporting with 61.6% instruction coverage (11,636 / 18,884 instructions)
  • Added Codecov integration to GitHub Actions CI pipeline
  • Added coverage exclusions for vendored code (nfschema, nf-core-utils)
  • Added comprehensive input validation and error handling to all utility classes
  • Added thread-safe logging with CopyOnWriteArrayList
  • Added support for DataflowQueue and DataflowVariable in channel utility functions
  • Added support for value channels in formatSamples() dataTypes parameter
  • Added coverage badges and testing documentation to README

Changed

  • Standardized all method comments to JavaDoc style with @param and @return tags
  • Refactored channel functions into separate utility classes following modular pattern
  • Changed formatSamples() signature to accept Object dataTypes instead of Integer to support value channels
  • Updated GitHub Actions workflow to generate and upload coverage reports
  • Enhanced JaCoCo configuration with proper exclusions and thresholds (60% minimum)

Testing

  • Coverage Metrics:
    • Instruction Coverage: 61.6%
    • Method Coverage: 65.4%
    • Class Coverage: 70.0%
    • Total Tests: 230 (all passing ✓)
  • Coverage Strategy:
    • Excluded vendored packages from coverage calculations
    • Set 60% minimum instruction coverage threshold
    • Automated coverage report generation on every test run
    • Integration with Codecov for trend tracking

Documentation

  • Created CLAUDE.md with comprehensive plugin architecture documentation
  • Updated docs/TESTING.md with current test coverage and all test suites
  • Created docs/CODECOV_SETUP.md with Codecov integration guide
  • Added testing section to README with coverage statistics and commands
  • Added CI status, coverage, and license badges to README

v1.0.8

  • Removed unused functions
  • Removed input parameters for bactopiaToolInputs since they are not needed

v1.0.4 - 1.0.7

  • Stuff happened -.-

v1.0.3

  • Expose the config options

v1.0.2

  • bump to latest nextflow gradle plugin version
  • pin to nextflow 25.10.0

Fixed

  • sample names that are integers

v1.0.1

Fixed

  • Fixed meta.name being null when using --samples, --accession or --accessions options.

v1.0.0

Initial release of the nf-bactopia plugin. This plugin replicates the functionality of the previous libraries in Bactopia, while being compatible with future releases of Nextflow (>= 25).