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

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

Changes:

• 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

• 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

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

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.

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