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Change Channel. to channel. in all Nextflow scripts #430

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jonasscheid merged 2 commits into from
Jan 8, 2026
Merged

Change Channel. to channel. in all Nextflow scripts #430

jonasscheid merged 2 commits into from
Jan 8, 2026

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Copilot AI commented Jan 8, 2026 •
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Updated channel factory method naming convention from uppercase Channel. to lowercase channel. across all Nextflow scripts per nf-core standards.

Changes

  • Updated main workflow (workflows/mhcquant.nf): Channel.empty(), Channel.topic()
  • Updated 6 subworkflows in subworkflows/local/: Channel.empty(), Channel.fromPath()
  • Updated 8 module test files: Channel.of(), Channel.fromList()

Example:

// Before
ch_versions = Channel.empty()
Channel.fromPath(params.fasta, checkIfExists: true)

// After
ch_versions = channel.empty()
channel.fromPath(params.fasta, checkIfExists: true)

16 files modified, 29 replacements total. No functional changes.

💡 You can make Copilot smarter by setting up custom instructions, customizing its development environment and configuring Model Context Protocol (MCP) servers. Learn more Copilot coding agent tips in the docs.

Copilot AI mentioned this pull request Jan 8, 2026
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Copilot AI changed the title [WIP] Merge template 351 into dev branch Change Channel. to channel. in all Nextflow scripts Jan 8, 2026
Copilot AI requested a review from jonasscheid January 8, 2026 15:08
@jonasscheid jonasscheid marked this pull request as ready for review January 8, 2026 15:17
@jonasscheid jonasscheid merged commit b889a26 into merge-template-351 Jan 8, 2026
8 of 13 checks passed
@jonasscheid jonasscheid deleted the copilot/sub-pr-429 branch January 8, 2026 15:19
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github-actions bot commented Jan 8, 2026 •
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit 1caec35

+| ✅ 295 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   3 tests had warnings |!
-| ❌   1 tests failed       |-
Details

❌ Test failures:

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-01-08 15:19:00

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@marissaDubbelaar marissaDubbelaar Awaiting requested review from marissaDubbelaar

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@jonasscheid jonasscheid jonasscheid approved these changes

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