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Remove empty outdirs #1612

Merged
merged 3 commits into from
Aug 5, 2024
Merged

Remove empty outdirs #1612

merged 3 commits into from
Aug 5, 2024

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FriederikeHanssen
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Nextflow creates output directory folders, if they are present in publishDir.path even if saveAs prevents actual publishing of the files. This PR moves parts of th results directory logic to saveAs to prevent empty output directories from being created.

@FriederikeHanssen FriederikeHanssen marked this pull request as ready for review August 5, 2024 12:28
FriederikeHanssen
FriederikeHanssen commented Aug 5, 2024
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github-actions bot commented Aug 5, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e48d9bd

+| ✅ 199 tests passed       |+
#| ❔  12 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 3.4.3
  • 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!

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • 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: .gitignore or .prettierignore
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
  • template_strings - template_strings
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-05 13:10:07

kenibrewer
kenibrewer approved these changes Aug 5, 2024
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LGTM

@FriederikeHanssen FriederikeHanssen merged commit fc7b47e into nf-core:dev Aug 5, 2024
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@kenibrewer kenibrewer kenibrewer approved these changes

@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse is a code owner

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@FriederikeHanssen @kenibrewer