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1.7 - Titanium Kangaroo
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@ewels ewels released this 07 Oct 13:59
· 9258 commits to master since this release
1.7
2d324b4
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PyPI package description

  • The readme should now be rendered properly on PyPI.

Tools helper code

  • The tools create command now sets up a TEMPLATE and a dev branch for syncing
  • Fixed issue 379
  • nf-core launch now uses stable parameter schema version 0.1.0
  • Check that PR from patch or dev branch is acceptable by linting
  • Made code compatible with Python 3.7
  • The download command now also fetches institutional configs from nf-core/configs
  • When listing pipelines, a nicer message is given for the rare case of a detached HEAD ref in a locally pulled pipeline. #297
  • The download command can now compress files into a single archive.
  • nf-core create now fetches a logo for the pipeline from the nf-core website

Syncing

  • Can now sync a targeted pipeline via command-line
  • Updated Blacklist of synced pipelines
  • Removed chipseq from Blacklist of synced pipelines
  • Fixed issue #314

Linting

  • If the container slug does not contain the nf-core organisation (for example during development on a fork), linting will raise a warning, and an error with release mode on

Template

  • Add new code for Travis CI to allow PRs from patch branches too
  • Fix small typo in central readme of tools for future releases
  • Small code polishing + typo fix in the template main.nf file
  • Header ANSI codes no longer print [2m to console when using -with-ansi
  • Switched to yaml.safe_load() to fix PyYAML warning that was thrown because of a possible exploit
  • Add nf-core citation
  • Add proper nf-core logo for tools
  • Add Quick Start section to main README of template
  • Fix Docker RunOptions to get UID and GID set in the template
  • Dockerfile now specifically uses the proper release tag of the nfcore/base image
  • Use file instead of new File
    to avoid weird behavior such as making an s3:/ directory locally when using
    an AWS S3 bucket as the --outdir.
  • Fix workflow.onComplete() message when finishing pipeline
  • Update URL for joining the nf-core slack to https://nf-co.re/join/slack
  • Increased default time limit to 4h
  • Add direct link to the pipeline slack channel in the contribution guidelines
  • Add contributions and support heading with links to contribution guidelines and link to the pipeline slack channel in the main README
  • Fix Parameters JSON due to new versionized structure
  • Added conda-forge::r-markdown=1.1 and conda-forge::r-base=3.6.1 to environment
  • Plain-text email template now has nf-core ASCII artwork
  • Template configured to use logo fetched from website
  • New option --email_on_fail which only sends emails if the workflow is not successful
  • Add file existence check when checking software versions
  • Fixed issue [https://github.com//issues/165] - Use checkIfExists
  • Consistent spacing for if statements
  • Add sensible resource labels to base.config

Other

  • Bump conda to 4.6.14 in base nf-core Dockerfile
  • Added a Code of Conduct to nf-core/tools, as only the template had this before
  • TravisCI tests will now also start for PRs from patch branches, to allow fixing critical issues without making a new major release
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