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Unhide params trim_fastq, umi_read_structure, and aligner.#1179

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robsyme merged 4 commits intonf-core:devfrom
robsyme:unhide-some-params
Aug 15, 2023
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Unhide params trim_fastq, umi_read_structure, and aligner.#1179
robsyme merged 4 commits intonf-core:devfrom
robsyme:unhide-some-params

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@robsyme robsyme commented Aug 14, 2023

Minor PR to unhide three parameters that are arguably used often enough to make the list of those made visible-by-default.

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/sarek 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>).
  • 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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Unhide params trim_fastq, umi_read_structure, and aligner.
7ab8c61 
Signed-off-by: Rob Syme <rob.syme@gmail.com>
@robsyme robsyme requested a review from maxulysse as a code owner August 14, 2023 20:48
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robsyme commented Aug 14, 2023

Addressing issue #1170

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github-actions bot commented Aug 14, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6a840e7

+| ✅ 151 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   2 tests had warnings |!
Details

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-15 11:00:18

FriederikeHanssen
FriederikeHanssen approved these changes Aug 14, 2023
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great, thanks :) Can you add it to the Changelog? Approving, because it is later here already

asp8200
asp8200 reviewed Aug 14, 2023
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Thanks, Rob

@robsyme @asp8200
Update nextflow_schema.json
b0d1248 
While here, remove backticks from Sarek and DragMap software names.

Co-authored-by: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com>
maxulysse
maxulysse reviewed Aug 15, 2023
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maxulysse
maxulysse reviewed Aug 15, 2023
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robsyme and others added 2 commits August 15, 2023 06:57
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Update nextflow_schema.json
cbe8ccd 
Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
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Update nextflow_schema.json
6a840e7 
Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
@robsyme robsyme merged commit f9fd774 into nf-core:dev Aug 15, 2023
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maxulysse commented Aug 15, 2023

What about the CHANGELOG?

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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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