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1.5 - Iron Shark
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@ewels ewels released this 13 Mar 22:16
1.5
1855d34
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Learn about vigilant mode.

Template pipeline

  • Dropped Singularity file
  • Summary now logs details of the cluster profile used if from nf-core/configs
  • Dockerhub is used in favor of Singularity Hub for pulling when using the Singularity profile
  • Changed default container tag from latest to dev
  • Brought the logo to life
  • Change the default filenames for the pipeline trace files
  • Remote fetch of nf-core/configs profiles fails gracefully if offline
  • Remove params.container and just directly define process.container now
  • Completion email now includes MultiQC report if not too big
  • params.genome is now checked if set, to ensure that it's a valid iGenomes key
  • Together with nf-core/configs, helper function now checks hostname and suggests a valid config profile

Tools helper code

  • New nf-core launch command to interactively launch nf-core pipelines from command-line

    • Works with a parameters.settings.json file shipped with each pipeline
    • Discovers additional params from the pipeline dynamically

  • Drop Python 3.4 support

  • nf-core list now only shows a value for "is local latest version" column if there is a local copy.

  • Lint markdown formatting in automated tests

    • Added markdownlint-cli for checking Markdown syntax in pipelines and tools repo

  • Syncing now reads from a blacklist.json in order to exclude pipelines from being synced if necessary.

  • Added nf-core tools API description to assist developers with the classes and functions available.

    • Docs are automatically built by Travis CI and updated on the nf-co.re website.

  • Introduced test for filtering remote workflows by keyword.

  • Build tools python API docs

    • Use Travis job for api doc generation and publish

  • nf-core bump-version now stops before making changes if the linting fails

  • Code test coverage

    • Introduced test for filtering remote workflows by keyword

  • Linting updates

    • Now properly searches for conda packages in default channels
    • Now correctly validates version pinning for packages from PyPI
    • Updates for changes to process.container definition

Other

  • Bump conda to 4.6.7 in base nf-core Dockerfile
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