Nf-core

Template pipeline

- Dropped Singularity file
- Summary now logs details of the cluster profile used if from [nf-core/configs](https://github.com/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
- `awsbatch` executor requires the `tracedir` not to be set to an `s3` bucket.

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](https://github.com/nf-core/tools/issues/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

- `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](https://github.com/nf-core/tools/issues/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](https://github.com/nf-core/tools/releases/tag/1.2) - [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](https://github.com/nf-core/tools/releases/tag/1.1) - [2018-08-14]

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

- The [Cookiecutter template](https://github.com/nf-core/cookiecutter) 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 cookiecutter 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](https://github.com/nf-core/tools/releases/tag/1.0.1) - [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](https://github.com/nf-core/tools/releases/tag/1.0) - [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