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1.8 - Black Sheep
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@drpatelh drpatelh released this 27 Jan 13:20
1.8
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Learn about vigilant mode.

Continuous integration

  • GitHub Actions CI workflows are now included in the template pipeline
    • Please update these files to match the existing tests that you have in .travis.yml
  • Travis CI tests will be deprecated from the next tools release
  • Linting will generate a warning if GitHub Actions workflows do not exist and if applicable to remove Travis CI workflow file i.e. .travis.yml.

Tools helper code

  • Refactored the template synchronisation code to be part of the main nf-core tool
  • nf-core bump-version now also bumps the version string of the exported conda environment in the Dockerfile
  • Updated Blacklist of synced pipelines
  • Ignore pre-releases in nf-core list
  • Updated documentation for nf-core download
  • Fixed typo in nf-core launch final command
  • Handle missing pipeline descriptions in nf-core list

Linting

  • Adjusted linting to enable patch branches from being tested
  • Warn if GitHub Actions workflows do not exist, warn if .travis.yml and circleCI are there
  • Lint for Singularity file and raise error if found #458
  • Added linting of GitHub Actions workflows linting.yml, ci.yml and branch.yml
  • Warn if pipeline name contains upper case letters or non alphabetical characters #85
  • Make CI tests of lint code pass for releases

Template pipeline

  • Fixed incorrect paths in iGenomes config as described in issue #418
  • Fixed incorrect usage of non-existent parameter in the template #446
  • Add UCSC genomes to igenomes.config and add paths to all genome indices
  • Change maxMultiqcEmailFileSize parameter to max_multiqc_email_size
  • Export conda environment in Docker file #349
  • Change remaining parameters from camelCase to snake_case #39
    • --singleEnd to --single_end
    • --igenomesIgnore to --igenomes_ignore
    • Having the old camelCase versions of these will now throw an error
  • Add autoMounts=true to default singularity profile
  • Add in markdownlint checks that were being ignored by default
  • Disable ansi logging in the travis CI tests
  • Move paramssection from base.config to nextflow.config
  • Use env scope to export PYTHONNOUSERSITE in nextflow.config to prevent conflicts with host Python environment
  • Bump minimum Nextflow version to 19.10.0 - required to properly use env scope in nextflow.config
  • Added support for nf-tower in the travis tests, using public mailbox nf-core@mailinator.com
  • Add link to Keep a Changelog and Semantic Versioning to CHANGELOG
  • Adjusted .travis.yml checks to allow for patch branches to be tested
  • Add Python 3.7 dependency to the environment.yml file
  • Remove awsbatch profile cf nf-core/configs#71
  • Make scrape_software_versions.py compatible with Python3 to enable miniconda3 in base image PR
  • Add GitHub Actions workflows and respective linting
  • Add NXF_ANSI_LOG as global environment variable to template GitHub Actions CI workflow
  • Fixed global environment variable in GitHub Actions CI workflow
  • Add --awscli parameter
  • Add README.txt path for genomes in igenomes.config nf-core/atacseq#75
  • Fix buggy ANSI codes in pipeline summary log messages
  • Add a TODO line in the new GitHub Actions CI test files

Base Docker image

  • Use miniconda3 instead of miniconda for a Python 3k base environment
    • If you still need Python 2 for your pipeline, add conda-forge::python=2.7.4 to the dependencies in your environment.yml
  • Update conda version to 4.7.12

Other

  • Updated Base Dockerfile to Conda 4.7.10
  • Entirely switched from Travis-Ci.org to Travis-Ci.com for template and tools
  • Improved core documentation (-profile)
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