Tools 0.4.5

• Fix how jobby parses slurm stdout/stderr files. (#122, @kopardev, @kelly-sovacool)
• The run_jobby_on_* scripts are now deprecated in favor of using jobby directly. (#123, @kelly-sovacool)
• Use miniforge3 installation on biowulf. (#124, @kelly-sovacool)

Tools 0.4.4

• Fixes for ccbr_tools install: (#98, @kelly-sovacool)
  • Correct installation method for spacesavers2.
  • Change symlink permissions so group members can edit them.
• Allow nextflow pipelines to specify walltime & memory usage for the slurm submission template. (#116, @kelly-sovacool)

Tools 0.4.3

• add standalone script to retrieve HPC cluster name. (#93, @kopardev)
• module_list now retrieves the full module version. (#93, @kopardev)

Tools 0.4.2

• Fix ccbr_tools install: add group write permissions after installation. (#89, @kelly-sovacool)
• Updates to nextflow.run(): (#90, @kelly-sovacool)
  • Allow pipelines to pass in module versions.
    • This is needed for the next version of champagne which will use nextflow v25 for the new output directive, while other pipelines will continue to use the default nextflow module version.
  • Ensure nextflow.run() stops if the nextflow preview errors out.

Tools 0.4.1

• Breaking change: Spooker now takes named options rather than positional arguments. (#85, @kelly-sovacool)
• jobby now omits log columns when the format is markdown, even if --outerr is used. (#86, @kopardev)
• Minor documentation improvements. (#81, @kelly-sovacool)

Tools 0.4.0

New features

• jobby overhaul (#59, #75, @kopardev)
  • Uses saccount to get slurm job information, which should work for any HPC running slurm.
  • Has options --tsv, --json, and --yaml to output the job information in those formats. If not specified, markdown is used.
  • Can accept a snakemake log file, nextflow log file, or a list of slurm job IDs as input.
  • Can include the job stdout/stderr log files (--outerr) for only failed jobs or all jobs (--include-completed). (#71, @kelly-sovacool)
• module_list is a new utility to list all loaded modules as JSON or retrieve the version of a specific module. (#63, @kopardev)
• ccbr_tools install has new options: (#60, @kelly-sovacool)
  • --type to specify the type of tool to install (e.g. PythonTool, BashTool, Snakemake, or Nextflow).
  • --hpc (e.g. biowulf, frce) to specify the HPC environment for debugging purposes.
• spooker updates:
  • Now accepts the path to the pipeline CLI as an optional argument. (#69, @kelly-sovacool)
  • Now bundles all pipeline information into a single gzipped JSON file. (#71, @kelly-sovacool)
    • A tar archive is no longer created, as only one file is now needed.
    • The tree & jobby information are included as strings in the JSON file.
• New shared conda environment on biowulf: py3.11-8 for ccbrpipeliner/8. (#79, @kelly-sovacool)

Bug fixes

• Fix ccbr_tools install: use relative paths for symlinks within the same directory. (#58, @kelly-sovacool)

Tools 0.3.2

• fix ccbr_tools install: use the full path to the conda env on biowulf. (#64, @kelly-sovacool)

Tools 0.3.1

• Bug fixes in ccbr_tools install:
  • ccbr_tools & ccbr_actions were using incorrect repo names. (#53, @kelly-sovacool)
  • absolute paths were not being used for the symlinks. (#55, @kelly-sovacool)
• Minor documentation improvements. (#54, @kelly-sovacool)

Tools 0.3.0

• Allow relaxed version with only major and minor components in match_semver() with strict_semver=False. (#49, @kelly-sovacool)
• Remove args and add repo parameter to get_latest_release_tag() and get_latest_release_hash(). (#51, @kelly-sovacool)

Tools 0.2.4

• Fix ccbr_tools.pipeline.nextflow.run: (#46, @kelly-sovacool)
  • make sure preview loads necessary modules.
  • improve stack trace when nextflow command fails.
• New theme templates based on the FNL branding guide: (#47, @kelly-sovacool)
  • mkdocs-fnl for websites built with mkdocs material.
  • pkgdown-fnl for R package websites built with pkgdown.
• Create helper to install software on supported HPCs.
  • usage: ccbr_tools install TOOL_NAME VERSION_TAG