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Set a default docker registry outside of profile scope. #1021

Merged
merged 3 commits into from
May 11, 2023
Merged

Set a default docker registry outside of profile scope. #1021

merged 3 commits into from
May 11, 2023

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robsyme
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@robsyme robsyme commented May 11, 2023

The docker.registry configuration should always be set, as running on cloud executors will need to pull docker images but will not necessarily use the docker profile.

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 - have you followed the pipeline conventions in the contribution docs- [ ] If necessary, also make a PR on the nf-core/rnaseq 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 --outdir <OUTDIR>).
  • 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).

@robsyme
Set a default docker registry outside of profile scope.
a350ca1 
The `docker.registry` configuration should always be set, as running
on cloud executors will need to pull docker images but will not
necessarily use the `docker` profile.
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github-actions bot commented May 11, 2023 •
edited
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit deffccb

+| ✅ 150 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • 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: lib/NfcoreSchema.groovy
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-05-11 09:17:49

@maxulysse
Update nextflow.config
deffccb 
restore process.shell declaration
@drpatelh drpatelh merged commit 62ed4d9 into dev May 11, 2023
@maxulysse maxulysse deleted the docker-registry-config-move branch May 11, 2023 12:54
@pinin4fjords pinin4fjords mentioned this pull request May 11, 2023
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@maxulysse maxulysse maxulysse approved these changes

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@robsyme @maxulysse @drpatelh