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fix nextflow_schema.json structure #279

Merged
merged 5 commits into from
Oct 26, 2024
Merged

fix nextflow_schema.json structure #279

merged 5 commits into from
Oct 26, 2024

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mashehu
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@mashehu mashehu commented Oct 23, 2024

Just guessed the section to put it in.
This parameter needs some documentation.

@mashehu mashehu requested a review from a team as a code owner October 23, 2024 11:56
@mashehu mashehu requested review from Aratz and removed request for a team October 23, 2024 11:56
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github-actions bot commented Oct 23, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 320037a

+| ✅ 202 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.5.2
  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • 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 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

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-24 15:13:17

@grst
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grst commented Oct 24, 2024

The "strandedness" is only used for downstream samplesheet generation, e.g. to specify strandedness for the nf-core/rnaseq samplesheet that is generated. It has no effect on the demux result.

@mashehu
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mashehu commented Oct 24, 2024

feel free to put it in the right section 🙂

mashehu
mashehu commented Oct 24, 2024
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nextflow_schema.json Outdated Show resolved Hide resolved
atrigila and others added 3 commits October 24, 2024 15:07
@atrigila
add enum options
5042a15
@atrigila @mashehu
Update nextflow_schema.json
6c9d47b 
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
@atrigila
fix comma
320037a
@nschcolnicov nschcolnicov self-requested a review October 25, 2024 14:13
nschcolnicov
nschcolnicov approved these changes Oct 25, 2024
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LGTM!

@atrigila atrigila merged commit 9e11c07 into dev Oct 26, 2024
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@nschcolnicov nschcolnicov nschcolnicov approved these changes

@Aratz Aratz Awaiting requested review from Aratz Aratz is a code owner automatically assigned from nf-core/demultiplex

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@mashehu @grst @nschcolnicov @atrigila