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Patch 1.0.2#68

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CaroAMN merged 20 commits into
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Jun 18, 2026
Merged

Patch 1.0.2#68
CaroAMN merged 20 commits into
masterfrom
dev

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@CaroAMN

@CaroAMN CaroAMN commented Jun 18, 2026

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PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/lsmquant branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

nf-core-bot and others added 17 commits April 28, 2026 11:21
@github-actions

github-actions Bot commented Jun 18, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b9cc44f

+| ✅ 214 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗  15 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • pipeline_todos - TODO string in README.md: update the following command to include all required parameters for a minimal example
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/lsmquant/lsmquant/lint_results.md: _* pipeline_if_empty_null - No ifEmpty(null) strings found
    _
  • schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-06-18 12:05:07

jonasscheid
jonasscheid approved these changes Jun 18, 2026
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Comment thread nextflow.config

// Nextflow plugins
plugins {
id 'nf-schema@2.5.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet

@jonasscheid jonasscheid Jun 18, 2026

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Fix to 2.7.2 in next release

@CaroAMN CaroAMN Jun 18, 2026

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thanks, It's on the list : #70 :)

@CaroAMN CaroAMN merged commit 6854d63 into master Jun 18, 2026
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@mashehu mashehu mashehu approved these changes
@jonasscheid jonasscheid jonasscheid approved these changes

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@CaroAMN @mashehu @jonasscheid @nf-core-bot