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CHANGELOG.md

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Changelog

All notable changes to pipeline-Nextflow-config.

The format is based on Keep a Changelog.

This project adheres to Semantic Versioning.

[Unreleased]

[1.3.0] - 2024-09-04

Added

  • sanitize_uclahs_cds_id function
  • Functional testing framework with concrete tests for methods.set_env()
  • Functional test for bam_parser.parse_bam_header()
  • Dump parameters with json_extractor.store_params_json()
  • Option to allow empty fields in a CSV to be parsed without error
  • Function to save process logs, even after failure

Fixed

  • Fix retry for potentially undefined variable proc_name_keys #57
  • Fix schema.check_write_permission when null is returned by getParentFile #59
  • Fix checking of choices to properly check choices when given

Changed

  • Allow set_resources_allocation to use maximum allocation values defined in params
  • Add defs to multiple variables that should not be globally defined
  • Allow specific schema validation function to accept pre-loaded schema as input
  • Add try-catch to schema validation to log the parameter being failed to validate
  • Rename check_bam_list function to more general check_readable_file_list
  • Allow Path schema type to be a GString

[1.2.0] - 2023-10-06

Added

  • Custom validation types and functions for BAMs

[1.1.0] - 2023-10-06

Added

  • Generic resource allocations for outside ucla_cds
  • get_absolute_path function to resolve a path relative to the current configu file
  • Function for merging publishDir rules
  • Check for empty lists
  • Function for specific schema validation
  • BAM parsing module
  • Funtion to update base resource allocation values
  • Env setting function
  • Function to use CPUs with Docker to circumvent behavior introduced by Nextflow starting in v22.11.0-edge
  • Function for resolving pipelines in metapipelines
  • Common functions for align-DNA and -RNA
  • Option for user to overwrite previously loaded custum types by calling schema.load_custom_types() with argument purge_existing_custom_types=true

Fixed

  • BAM parser failing if multiple lines needed to be skipped
  • Schema config function load_custom_types() overwriting previously loaded custom types if called multiple times
  • workDir parity to handle NXF_WORK setting

Changed

  • Modify exceptions to be more specific

[1.0.0] - 2022-08-24

Added

  • Retry module
  • Schema validation module
  • Check for empty strings
  • CSV parsing module
  • Common methods module
  • Registered output directory generation function
  • Error handling for node-specific configs
  • Reference genome version extraction function

Changed

  • Initial repo set up
  • Generalize error message
  • Clarify retry README