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File structure for results should be coherent between reports and preprocessing#653

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FriederikeHanssen merged 5 commits intonf-core:devfrom
FriederikeHanssen:file_structure
Jul 18, 2022
Merged

File structure for results should be coherent between reports and preprocessing#653
FriederikeHanssen merged 5 commits intonf-core:devfrom
FriederikeHanssen:file_structure

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@FriederikeHanssen
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@FriederikeHanssen FriederikeHanssen commented Jul 18, 2022

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).

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maxulysse commented Jul 18, 2022

CHANGELOG.md please?

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github-actions Bot commented Jul 18, 2022 •
edited
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 570a357

+| ✅ 146 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!
Details

❗ 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 2022-07-18 15:34:30

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maxulysse commented Jul 18, 2022

issue with alignment_to_fastq test

maxulysse
maxulysse approved these changes Jul 18, 2022
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LGTM, but better be safe than sorry and wait until all ✔️ before merging

@FriederikeHanssen FriederikeHanssen merged commit 0bf6676 into nf-core:dev Jul 18, 2022
@FriederikeHanssen FriederikeHanssen deleted the file_structure branch July 10, 2023 19:00
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