All pull requests

Pull requests

• fix: keep the full name of local TOOL/SUBTOOL components

  #4541·awgymer opened Oct 23, 2026Contributor·2 of 4 tasks·

  ·
  2

• remove unnecessary default branch detection from sync action

  #4540·mashehu opened Oct 22, 2026Member·

  ·
  1

• fix(lint): explain missing ontology mapping keys (#3846)

  #4539·harshitethic opened Oct 22, 2026·

  ·
  1

• fix(lint): support named local subworkflows (#4049)

  #4538·harshitethic opened Oct 22, 2026·

  ·
  1

• fix(lint): skip local .venv when checking merge markers (#3420)

  #4537·harshitethic opened Oct 22, 2026·

  ·
  1

• fix(template): preserve version strings in topic YAML (#4500)

  #4536·harshitethic opened Oct 22, 2026·

  ·

• Update dependency java-jdk to v25

  #4535·renovate[bot] opened Oct 22, 2026Bot·1 task·

  ·
  2

• fix(component): fix included component names for external orgs

  #4531·prototaxites opened Oct 20, 2026Contributor·1 of 4 tasks·

  ·

  · 4.3.0
  1

• Experimental: scaffold AWS full test output snapshots

  #4524·adamrtalbot opened Oct 16, 2026Contributor·3 of 4 tasks·

  ·
  1

• Overhaul pipeline template docs structure

  #4522·jfy133 opened Oct 16, 2026Member·4 tasks·

  ·
  1

• Apply template updates as migrations in sync PRs

  #4520·Skitionek opened Oct 15, 2026·3 tasks done·

  ·
  2

• Resolve template merge conflicts in nf-core pipelines sync

  #4519·paulinefx opened Oct 15, 2026·

  ·
  4

• Update AWS Megatest Launch Action

  #4518·FriederikeHanssen opened Oct 15, 2026Contributor·4 tasks·

  ·

  · 4.3.0
  14

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

  #4517·harshitethic opened Oct 13, 2026·3 of 4 tasks·

  ·
  1

  1

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

  #4516·harshitethic opened Oct 13, 2026·

  ·

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

  #4513·harshitethic opened Oct 10, 2026·

  ·
  1

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

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

  ·
  1

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

  #4511·jfy133 opened Oct 9, 2026Member·

  ·

  · 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·

  ·

  · 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·

  ·

  · 4.3.0
  1

  5

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

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

  ·

  · 4.3.0
  1

  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·

  ·

  · 4.3.0

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

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

  ·
  7

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

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

  ·

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

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

  ·
  6