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CHANGELOG.md

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nf-core/tools: Changelog

v1.4 - 2018-12-12 Tantalum Butterfly

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

v1.3 - 2018-11-21

  • nf-core create command line interface updated
    • Interactive prompts for required arguments if not given
    • New flag for workflow author
  • Updated channel order for bioconda/conda-forge channels in environment.yaml
  • Increased code coverage for sub command create and licenses
  • Fixed nasty dependency hell issue between pytest and py package in Python 3.4.x
  • Introduced .coveragerc for pytest-cov configuration, which excludes the pipeline template now from being reported
  • Fix 189: Check for given conda and PyPi package dependencies, if their versions exist
  • Added profiles for cfc,binac, uzh that can be synced across pipelines
    • Ordering alphabetically for profiles now
  • Added pip install --upgrade pip to .travis.yml to update pip in the Travis CI environment

v1.2 - 2018-10-01

  • Updated the nf-core release command
    • Now called nf-core bump-versions instead
    • New flag --nextflow to change the required nextflow version instead
  • Template updates
    • Simpler installation of the nf-core helper tool, now directly from PyPI
    • Bump minimum nextflow version to 0.32.0 - required for built in manifest.nextflowVersion check and access to workflow.manifest variables from within nextflow scripts
    • New withName syntax for configs
    • Travis tests fail if PRs come against the master branch, slightly refactored
    • Improved GitHub contributing instructions and pull request / issue templates
  • New lint tests
    • .travis.yml test for PRs made against the master branch
    • Automatic --release option not used if the travis repo is nf-core/tools
    • Warnings if depreciated variables params.version and params.nf_required_version are found
  • New nf-core licences subcommand to show licence for each conda package in a workflow
  • nf-core list now has options for sorting pipeline nicely
  • Latest version of conda used in nf-core base docker image
  • Updated PyPI deployment to correctly parse the markdown readme (hopefully!)
  • New GitHub contributing instructions and pull request template

v1.1 - 2018-08-14

Very large release containing lots of work from the first nf-core hackathon, held in SciLifeLab Stockholm.

  • The Cookiecutter template has been merged into tools
    • The old repo above has been archived
    • New pipelines are now created using the command nf-core create
    • The nf-core template and associated linting are now controlled under the same version system
  • Large number of template updates and associated linting changes
    • New simplified cookicutter variable usage
    • Refactored documentation - simplified and reduced duplication
    • Better manifest variables instead of params for pipeline name and version
    • New integrated nextflow version checking
    • Updated travis docker pull command to use tagging to allow release tests to pass
    • Reverted Docker and Singularity syntax to use ENV hack again
  • Improved Python readme parsing for PyPI
  • Updated Travis tests to check that the correct dev branch is being targeted
  • New sync tool to automate pipeline updates
    • Once initial merges are complete, a nf-core bot account will create PRs for future template updates

v1.0.1 - 2018-07-18

The version 1.0 of nf-core tools cannot be installed from PyPi. This patch fixes it, by getting rid of the requirements.txt plus declaring the dependent modules in the setup.py directly.

v1.0 - 2018-06-12

Initial release of the nf-core helper tools package. Currently includes four subcommands:

  • nf-core list: List nf-core pipelines with local info
  • nf-core download: Download a pipeline and singularity container
  • nf-core lint: Check pipeline against nf-core guidelines
  • nf-core release: Update nf-core pipeline version number