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Reply reviewer's comment for 2.0.0#745

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atrigila merged 23 commits into
nf-core:devfrom
atrigila:release_review_replies
Jun 22, 2026
Merged

Reply reviewer's comment for 2.0.0#745
atrigila merged 23 commits into
nf-core:devfrom
atrigila:release_review_replies

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@atrigila

@atrigila atrigila commented Jun 17, 2026 •
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The changes in this PR address the following reviewer's comments:

  • Are *.{limma,dream}.{results,results_filtered,annotated}.tsv still inconsistent with the seed set?
    Now they are consistent, as previously decoupler and dream were not using the parameter round_digits, which therefore caused some results to be unstable.
  • In docs/usage.md it might be good to provide small snippets of what the different matrix/input files look like to help if users aren't sure which to go with?

For #744

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github-actions Bot commented Jun 17, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d29651d

+| ✅ 410 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗  12 tests had warnings |!
Details

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.0.0
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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 base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • schema_lint - Parameter input is not defined in the correct subschema (input_output_options)
  • schema_description - No description provided in schema for parameter: dream_p_value
  • schema_description - No description provided in schema for parameter: dream_lfc

❔ Tests ignored:

  • files_exist - File is ignored: assets/multiqc_config.yml
  • nextflow_config - Config default ignored: params.report_file
  • nextflow_config - Config default ignored: params.logo_file
  • nextflow_config - Config default ignored: params.css_file
  • nextflow_config - Config default ignored: params.citations_file
  • files_unchanged - File ignored due to lint config: assets/nf-core-differentialabundance_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-differentialabundance_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-differentialabundance_logo_dark.png
  • multiqc_config - multiqc_config

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-06-22 13:58:20

@atrigila atrigila mentioned this pull request Jun 19, 2026
Merged
@atrigila atrigila marked this pull request as ready for review June 22, 2026 14:26
@atrigila atrigila requested a review from grst June 22, 2026 14:27
@atrigila atrigila merged commit b95f754 into nf-core:dev Jun 22, 2026
58 checks passed
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@grst grst grst approved these changes

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@atrigila @grst