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Use --skip_preseq by default#521

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Kevin-Brockers merged 4 commits into
nf-core:devfrom
JoseEspinosa:updates
Jun 30, 2026
Merged

Use --skip_preseq by default#521
Kevin-Brockers merged 4 commits into
nf-core:devfrom
JoseEspinosa:updates

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@JoseEspinosa

@JoseEspinosa JoseEspinosa commented Jun 30, 2026

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Make skip_preseq the default option.

Closes #456

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core 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>).
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions Bot commented Jun 30, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6470f12

+| ✅ 271 tests passed       |+
#| ❔   5 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   8 tests had warnings |!
Details

❗ Test warnings:

  • 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 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 base.config: Check the defaults for all processes

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.bamtools_filter_pe_config
  • nextflow_config - Config default ignored: params.bamtools_filter_se_config
  • files_unchanged - File ignored due to lint config: assets/nf-core-chipseq_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-chipseq_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-06-30 13:08:42

@JoseEspinosa JoseEspinosa marked this pull request as ready for review June 30, 2026 13:41
@JoseEspinosa JoseEspinosa mentioned this pull request Jun 30, 2026
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Kevin-Brockers
Kevin-Brockers approved these changes Jun 30, 2026
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@Kevin-Brockers Kevin-Brockers left a comment

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Looks good to me!

@Kevin-Brockers Kevin-Brockers merged commit c1786b3 into nf-core:dev Jun 30, 2026
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@Kevin-Brockers Kevin-Brockers Kevin-Brockers approved these changes

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@JoseEspinosa @Kevin-Brockers