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Nextflow_schema.json updates #646

Merged
merged 12 commits into from
Jul 17, 2022
Merged

Nextflow_schema.json updates #646

merged 12 commits into from
Jul 17, 2022

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FriederikeHanssen
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close #502

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 - add to the software_versions process and a regex to scrape_software_versions.py
    • 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).
  • 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).

maxulysse
maxulysse reviewed Jul 17, 2022
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github-actions bot commented Jul 17, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 093a35f

+| ✅ 145 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-07-17 14:02:01

@maxulysse
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What's happening with all the ascat params?

FriederikeHanssen and others added 2 commits July 17, 2022 15:11
@FriederikeHanssen
update icons, (it's important:joy: :sparkle:
5491bea
@FriederikeHanssen @maxulysse
Update nextflow_schema.json
52a9237 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
@FriederikeHanssen
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What's happening with all the ascat params?

Reorganized them a bit, some are ref files but some are tool configurations.
Also removed ascat_chromosomes, since you can't actually manipualte it form the command line. It is used like this currently in the modules.config:

            "chrom_names": meta.sex == 'XX' ? params.ascat_chromosomes : "c(1:22, 'X', 'Y')",

@FriederikeHanssen FriederikeHanssen marked this pull request as ready for review July 17, 2022 13:17
@maxulysse
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Can you update CHANGELOG?

maxulysse
maxulysse reviewed Jul 17, 2022
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@FriederikeHanssen @maxulysse
Update nextflow_schema.json
b6ccbfd 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
maxulysse
maxulysse reviewed Jul 17, 2022
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maxulysse
maxulysse reviewed Jul 17, 2022
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@FriederikeHanssen @maxulysse
Update nextflow_schema.json
2f87020 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
maxulysse
maxulysse reviewed Jul 17, 2022
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I noticed that we sometimes have \n\n and sometimes \n.
What about putting more consistency there.

@maxulysse
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You have a conflict in CHANGELOG

@maxulysse maxulysse merged commit 5dc3f3b into nf-core:dev Jul 17, 2022
@FriederikeHanssen FriederikeHanssen mentioned this pull request Jul 18, 2022
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@maxulysse maxulysse maxulysse approved these changes

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@FriederikeHanssen @maxulysse