All pull requests

Pull requests

• fix(lint): resolve simple params references in schema defaults

  #4517·harshitethic opened Oct 13, 2026·

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  1

• fix(pipelines): ignore local Pixi environments during lint and sync

  #4516·harshitethic opened Oct 13, 2026·

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• bump to 4.2.0

  #4514·mashehu opened Oct 12, 2026Member·

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  · 4.2.0
  1

• fix(github): avoid false missing-token warning and give login guidance

  #4513·harshitethic opened Oct 10, 2026·

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  1

• Do not load wf config caches written in the old -flat format

  #4512·raashish1601 opened Oct 10, 2026·3 tasks done·

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  1

• Add license header to module and subworkflow main.nf templates

  #4511·jfy133 opened Oct 9, 2026Member·

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  · 4.3.0
  7

• Template: finish rather than terminate when a task runs out of retries

  #4506·erikrikarddaniel opened Oct 8, 2026Member·2 tasks done·

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  · 4.3.0
  1

• Add ${params.XXX} and ${projectDir} interpolation when comparing schema and config default params values.

  #4505·LouisLeNezet opened Oct 8, 2026Contributor·4 tasks·

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  · 4.3.0
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  5

• Add -w/--fail-warned to nf-core pipelines schema lint

  #4503·qiaobochi040726-source opened Oct 8, 2026·

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  · 4.3.0
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  1

• refractor: add nf-schema comment to the plugin import and sample sheet channel generation

  #4497·rarestpreet opened Oct 6, 2026·2 of 4 tasks·

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  · 4.3.0

• Add a pre-commit hook that disallows the .view() operator

  #4496·prototaxites opened Oct 5, 2026Contributor·4 tasks·

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  7

• Skip files_unchanged lint when no author names are found in the manifest

  #4495·srikarjy opened Oct 3, 2026·3 of 4 tasks·

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• fix(lint): respect ignore_configs for multiqc_config's export_plots check

  #4492·jtremblay opened Oct 2, 2026·1 of 4 tasks·

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  6

• Skip included names that are not installed components when recreating installed_by

  #4491·pinin4fjords opened Oct 2, 2026Member·4 tasks done·

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  7

• Only run subsequent steps if branch-deploy.outputs.continue is true

  #4480·kevinbackhouse opened Sep 24, 2026Contributor·4 tasks·

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  1

• Template: add metro-map workflow diagram feature

  #4478·ewels opened Sep 21, 2026Member·4 of 5 tasks·

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  · 4.3.0
  3

• Preserve hand-written entries when regenerating container configs

  #4476·pinin4fjords opened Sep 21, 2026Member·5 tasks done·

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  · 4.3.0
  2

• Add docs_pages lint test

  #4475·erikrikarddaniel opened Sep 19, 2026Member·4 tasks done·

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  · 4.3.0
  1

• fix: validate manifest.name format when loading pipeline config

  #4470·kokhlo opened Sep 15, 2026·

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  1

  7

• Signal EDAM load failure and widen the extension map

  #4469·TilakSharma07 opened Sep 11, 2026·

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  1

• fix: guard against empty pipeline name in files_exist lint

  #4466·abhi-0203 opened Sep 7, 2026·

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  1

• modules bump-versions: match nf-core container formatting in main.nf

  #4459·asharaali opened Aug 31, 2026·

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  2

• Round-trip ci: block in .nf-core.yml

  WIP
  #4453·ewels opened Aug 24, 2026Member·3 of 4 tasks·

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  1

• Fix/4447 linting supressed

  #4450·JulianFlesch opened Aug 20, 2026Contributor·4 tasks·

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  · 4.2.0
  4

  

• Remove ext.use_gpu remnants (superseded by task.accelerator)

  #4445·mahesh-panchal opened Aug 17, 2026Member·

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  3