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@ewels ewels released this 04 Oct 21:51
· 3632 commits to master since this release
2.6
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Learn about vigilant mode.

⚠️ Please read

This release goes together with a major update on nf-core/modules that restructures DSL2 module files and updates the syntax of modules.json.

These changes have been brought about to accommodate the imminent release of shared subworkflows.

Please be aware of some points:

  • ♻️ You will need to run nf-core modules update on your pipeline which should move a lot of files around
  • 💀 Any module .patch files from nf-core modules patch may be lost (if you have any). Please take care to regenerate them.

If you have any issues, please drop us a line on Slack on the #tools channel 👍🏻

Template

  • Add actions/upload-artifact step to the awstest workflows, to expose the debug log file
  • Add prettier as a requirement to Gitpod Dockerimage
  • Bioconda incompatible conda channel setups now result in more informative error messages (#1812)
  • Update MultiQC module, update supplying MultiQC default and custom config and logo files to module
  • Add a 'recommend' methods description text to MultiQC to help pipeline users report pipeline usage in publications (#1749)
  • Fix template spacing modified by JINJA (#1830)
  • Fix MultiQC execution on template #1855
  • Don't skip including base.config when skipping nf-core/configs

Linting

  • Pipelines: Check that the old renamed lib files are not still present:
    • Checks.groovy -> Utils.groovy
    • Completion.groovy -> NfcoreTemplate.groovy
    • Workflow.groovy -> WorkflowMain.groovy

General

  • Add function to enable chat notifications on MS Teams, accompanied by hook_url param to enable it.
  • Schema: Remove allOf if no definition groups are left.
  • Use contextlib to temporarily change working directories (#1819)
  • More helpful error messages if nf-core download can't parse a singularity image download

Modules

  • If something is wrong with the local repo cache, offer to delete it and try again (#1850)
  • Restructure code to work with the directory restructuring in modules (#1859)
  • Make label: process_single default when creating a new module

Full Changelog

2.5.1...2.6

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