sanger-tol/treeval: 1.4.0 - Ancient Hippaforalkus

Enhancements & Fixes

• NF-Core template upgrade to 3.3.1.
  • Pipeline now uses NF-Schema for input validation.
  • Pipeline now uses nf-test for local and CI testing.
• Updating the structure of modules and subworkflows to follow new standards.
• Updating Channel names to follow new standards.
• Addition of run_hires flag (boolean) to control use of the hires pretext modules.
• Removal of unused modules such as avgcov, the average coverage module.
• Addition of the mode parameter, to replace the depreciating -entry flag.
  • Mode lists are 'include' lists, listing the processes needed per run.
• Removing entry points has significantly simplified the pipeline; mode now controls a set of steps for pipeline execution.
• Addition of specified reads.
  • Longreads and HiC are now specified in the input yaml file. Details in the usage document.
  • Longread and HiC data can optionally take a fofn (file of file names) where each line contains one file, see YAML_INPUT function fn_get_validated_channel.
  • NOTE: in cases where the same file is in both the fofn and a supplied list, the pipeline will exit with an error which will be detailed in the nextflow.log file.
• Corrected input values.
• SummaryStats Code has been removed, this will be replaced by a plugin in the future!
• Replace 5 modules with GAWK instead of cat | sed pattern modules.
• Simplification of the YAML_INPUT subworkflow.
• Removal of GrabFiles and replacement with the newer .resolve().
• Cleaning up of it -> it[0] into the more correct _meta, file -> file pattern.
• Moved GAWK commands into their own awk script files, this cleans up modules.config.
  • Added my_abs function to the GAWK_REFORMAT_INTERSECT to caluclate difference between start and end.
• Added [TreeVal:Error] and [TreeVal:Info] into intentional print statements to make it easier to see on the CLI and to search for in logs.

New Contributors

• @mahesh-panchal made their first contribution in https://github.com/sanger-tol/treeval/pull/412

Full Changelog: https://github.com/sanger-tol/treeval/compare/1.3.0...1.4.0