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v1.14 - Brass Chicken 🐔
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@ewels ewels released this 11 May 11:08
1.14
7721f37
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Template

  • Fixed an issue regarding explicit disabling of unused container engines [#972]
  • Removed trailing slash from params.igenomes_base to yield valid s3 paths (previous paths work with Nextflow but not aws cli)
  • Added a timestamp to the trace + timetime + report + dag filenames to fix overwrite issue on AWS
  • Rewrite the params_summary_log() function to properly ignore unset params and have nicer formatting [#971]
  • Fix overly strict --max_time formatting regex in template schema [#973]
  • Convert d to day in the cleanParameters function to make Duration objects like 2d pass the validation [#858]
  • Added nextflow version to quick start section and adjusted nf-core bump-version [#1032]
  • Use latest stable Nextflow version 21.04.0 for CI tests instead of the -edge release

Download

  • Fix bug in nf-core download where image names were getting a hyphen in nf-core which was breaking things.
  • Extensive new interactive prompts for all command line flags [#1027]
    • It is now recommended to run nf-core download without any cli options and follow prompts (though flags can be used to run non-interactively if you wish)
  • New helper code to set $NXF_SINGULARITY_CACHEDIR and add to .bashrc if desired [#1027]

Launch

  • Strip values from nf-core launch web response which are False and have no default in the schema [#976]
  • Improve API caching code when polling the website, fixes noisy log message when waiting for a response [#1029]
  • New interactive prompts for pipeline name [#1027]

Modules

  • Added tool_name_underscore to the module template to allow TOOL_SUBTOOL in main.nf [#1011]
  • Added --conda-name flag to nf-core modules create command to allow sidestepping questionary [#988]
  • Extended nf-core modules lint functionality to check tags in test.yml and to look for a entry in the pytest_software.yml file
  • Update modules commands to use new test tag format tool/subtool
  • New modules lint test comparing the functions.nf file to the template version
  • Modules installed from alternative sources are put in folders based on the name of the source repository

Linting

  • Fix bug in nf-core lint config skipping for the nextflow_config test [#1019]
  • New -k/--key cli option for nf-core lint to allow you to run only named lint tests, for faster local debugging
  • Merge markers lint test - ignore binary files, allow config to ignore specific files [#1040]
  • New lint test to check if all defined pipeline parameters are mentioned in main.nf [#1038]
  • Added fix to remove warnings about params that get converted from camelCase to camel-case [#1035]
  • Added pipeline schema lint checks for missing parameter description and parameters outside of groups [#1017]

General

  • Try to fix the fix for the automated sync when we submit too many PRs at once [#970]
  • Rewrite how the tools documentation is deployed to the website, to allow multiple versions
  • Created new Docker image for the tools cli package - see installation docs for details [#917]
  • Ignore permission errors for setting up requests cache directories to allow starting with an invalid or read-only HOME directory
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