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1.4 - Tantalum Butterfly
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@sven1103 sven1103 released this 12 Dec 15:39
· 9761 commits to master since this release
1.4
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Template pipeline

  • Institutional custom config profiles moved to github nf-core/configs
    • These will now be maintained centrally as opposed to being shipped with the pipelines in conf/
    • Load base.config by default for all profiles
    • Removed profiles named standard and none
    • Added parameter --igenomesIgnore so igenomes.config is not loaded if parameter clashes are observed
    • Added parameter --custom_config_version for custom config version control. Can use this parameter to provide commit id for reproducibility. Defaults to master
    • Deleted custom configs from template in conf/ directory i.e. uzh.config, binac.config and cfc.config
  • multiqc_config and output_md are now put into channels instead of using the files directly (see issue #222)
  • Added local.md to cookiecutter template in docs/configuration/. This was referenced in README.md but not present.
  • Major overhaul of docs to add/remove parameters, unify linking of files and added description for providing custom configs where necessary
  • Travis: Pull the dev tagged docker image for testing
  • Removed UPPMAX-specific documentation from the template.

Tools helper code

  • Make Travis CI tests fail on pull requests if the CHANGELOG.md file hasn't been updated
  • Minor bugfixing in Python code (eg. removing unused import statements)
  • Made the web requests caching work on multi-user installations
  • Handle exception if nextflow isn't installed
  • Linting: Update for Travis: Pull the dev tagged docker image for testing
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