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Update Fix docker.userEmulation Removal #25

Merged
merged 7 commits into from
Nov 5, 2024
Merged

Update Fix docker.userEmulation Removal #25

merged 7 commits into from
Nov 5, 2024

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sgsutcliffe
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@sgsutcliffe sgsutcliffe commented Oct 24, 2024 •
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The setting in the docker profile docker.userEmulation was removed from Nextflow in this PR 4596.

Following this issue I had implemented this at the process level as in this PR

process.containerOptions = '-u $(id -u):$(id -g)'

This caused problems when running on Azure but not locally, and was missed in tests.

However the correct solution, as seen in the nf-core template, here is to put it in the docker profile as via docker.runOptions = '-u $(id -u):$(id -g)'
e.g,

docker {
        docker.enabled         = true
        conda.enabled          = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
        apptainer.enabled      = false
        docker.runOptions      = '-u $(id -u):$(id -g)'
    }

PR checklist

  • This comment contains a description of changes (with reason).
  • Test in IRIDA-Next
  • Test on Azure
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).

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github-actions bot commented Oct 24, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ca5ca1f

+| ✅ 143 tests passed       |+
#| ❔  28 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-arboratornf_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-arboratornf_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-arboratornf_logo_dark.png
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: lib/Utils.groovy
  • files_exist - File is ignored: lib/WorkflowMain.groovy
  • files_exist - File is ignored: lib/NfcoreTemplate.groovy
  • files_exist - File is ignored: lib/WorkflowSnvphylnfc.groovy
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • nextflow_config - Config variable ignored: params.max_cpus
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: assets/nf-core-arboratornf_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-arboratornf_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-arboratornf_logo_dark.png
  • files_unchanged - File ignored due to lint config: docs/README.md
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/arboratornf/arboratornf/.github/workflows/awstest.yml
  • actions_awsfulltest - actions_awsfulltest
  • pipeline_name_conventions - pipeline_name_conventions

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.1
  • Run at 2024-11-05 14:49:26

@sgsutcliffe sgsutcliffe requested a review from apetkau October 30, 2024 17:37
apetkau
apetkau requested changes Oct 31, 2024
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Thanks so much Steven. This looks great 😄

Just one in-line comment.

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apetkau
apetkau approved these changes Oct 31, 2024
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Thanks so much 😄

@sgsutcliffe sgsutcliffe merged commit 317fd13 into dev Nov 5, 2024
4 checks passed
@sgsutcliffe sgsutcliffe deleted the test-azure-container-issue branch November 5, 2024 14:57
@sgsutcliffe sgsutcliffe mentioned this pull request Nov 5, 2024
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@apetkau apetkau apetkau approved these changes

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@sgsutcliffe @apetkau