Nextflow-config v1.3.0

What's Changed

• Autofix broken Confluence links by @nwiltsie in #42
• Add functional testing framework by @nwiltsie in #41
• Add documentation about tests, runner script by @nwiltsie in #44
• Add toy SAM/BAM files, add test for bam_parser.parse_bam_header by @nwiltsie in #46
• Add method to store params by @j2salmingo in #43
• Fix retry to force proc_name_set as a local variable by @zhuchcn in #58
• add sanitize_string function by @sorelfitzgibbon in #55
• Use params in set_resources_allocation by @yashpatel6 in #60
• Add defs to incorrectly-global variables by @nwiltsie in #61
• Add more options for specific validation function by @yashpatel6 in #63
• Upgrade to latest static analysis Action by @nwiltsie in #65
• Fix schema to handle error by @zhuchcn in #66
• Add method to always capture process log files by @nwiltsie in #64
• Empty fields in CSV by @yashpatel6 in #67
• Add GString to acceptable schema types for 'Path' by @nwiltsie in #69
• Generalize function for checking list of readable files by @yashpatel6 in #68
• Fix choices by @yashpatel6 in #71

New Contributors

• @zhuchcn made their first contribution in #58

Full Changelog: v1.2.0...v1.3.0

Nextflow-config v1.2.0

CHANGELOG

Added

• Custom validation types and functions for BAMs

Nextflow-config v1.1.0

CHANGELOG

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

Nextflow-config v1.0.0

CHANGELOG

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