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Important! Template update for nf-core/tools v2.11 #1360

Merged
merged 7 commits into from Dec 20, 2023
Merged

Important! Template update for nf-core/tools v2.11 #1360

merged 7 commits into from Dec 20, 2023

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nf-core-bot
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Version 2.11 of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-2.11 branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.

For instructions on how to merge this PR, please see https://nf-co.re/docs/contributing/sync/.

For more information about this release of nf-core/tools, please see the v2.11 release page.

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github-actions bot commented Dec 20, 2023 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ab9ade1

+| ✅ 148 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in WorkflowSarek.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/modules.config
  • 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
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_ci - actions_ci
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.11
  • Run at 2023-12-20 08:49:20

FriederikeHanssen
FriederikeHanssen reviewed Dec 20, 2023
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nextflow.config
@@ -190,6 +192,7 @@ profiles {
docker.userEmulation = { params.use_gatk_spark ? false : true }.call()
podman.enabled = false
shifter.enabled = false
docker.runOptions = '-u $(id -u):$(id -g)'
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I am getting anxious about any spark related issues :D

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a bit too, we'd need to try this out properly, I'll make an issue

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#1362

@maxulysse maxulysse mentioned this pull request Dec 20, 2023
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@maxulysse maxulysse merged commit 490c68c into dev Dec 20, 2023
23 checks passed
@maxulysse maxulysse deleted the nf-core-template-merge-2.11 branch December 20, 2023 08:59
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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

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@nf-core-bot @maxulysse @FriederikeHanssen