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Issue #456, set skip_preseq default to true, and updated docs and changelog#488

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Zashraf783 wants to merge 2 commits intonf-core:devfrom
Zashraf783:skip_preseq-default-true
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Issue #456, set skip_preseq default to true, and updated docs and changelog#488
Zashraf783 wants to merge 2 commits intonf-core:devfrom
Zashraf783:skip_preseq-default-true

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@Zashraf783
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@Zashraf783 Zashraf783 commented Mar 12, 2026

PR checklist

  • [O] 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/chipseq branch on the nf-core/test-datasets repository.
  • 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>).
  • 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).

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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @Zashraf783,

It looks like this pull-request is has been made against the Zashraf783/chipseq master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the Zashraf783/chipseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

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@JoseEspinosa JoseEspinosa left a comment

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Thanks for the contribution!I
The PR should be done against dev as you can see in the branch protection message and your branch should checkout from dev. Also I added some suggestions.


### Enhancements & fixes

- [[#456] (https://github.com/nf-core/chipseq/issues/456)] - Changed default for `--skip_preseq` to `true` (Preseq analysis is now skipped by default).
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This should be moved under the development version of the pipeline, this enhancements correspond to the released version 2.1.0

"skip_preseq": {
"type": "boolean",
"description": "Skip Preseq.",
"description": "Skip Preseq (true by default).",
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Suggested change
"description": "Skip Preseq (true by default).",
"description": "Skip Preseq.",

"type": "boolean",
"description": "Skip Preseq.",
"description": "Skip Preseq (true by default).",
"fa_icon": "fas fa-fast-forward"
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Suggested change
"fa_icon": "fas fa-fast-forward"
"fa_icon": "fas fa-fast-forward",
"default": true

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
@Zashraf783 Zashraf783 changed the base branch from master to dev March 13, 2026 23:02
@Zashraf783 Zashraf783 requested a review from JoseEspinosa March 13, 2026 23:04
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2 participants