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dropped quay.io from docker paths #94

Merged
merged 10 commits into from
Aug 30, 2024
Merged

dropped quay.io from docker paths #94

merged 10 commits into from
Aug 30, 2024

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mattheww95
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Removed docker quay.io tags.

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This PR is against the main branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @mattheww95,

It looks like this pull-request is has been made against the phac-nml/mikrokondo main branch.
The main branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to main are only allowed if they come from the phac-nml/mikrokondo dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

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github-actions bot commented Jul 11, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0419a5a

+| ✅ 223 tests passed       |+
#| ❔  31 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 0.3.0
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • schema_lint - Schema $id should be https://raw.githubusercontent.com/phac-nml/mikrokondo/master/nextflow_schema.json
    Found https://raw.githubusercontent.com/phac-nml/mikrokondo/main/nextflow_schema.json

❔ Tests ignored:

  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-mikrokondo_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-mikrokondo_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-mikrokondo_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: docs/output.md
  • files_exist - File is ignored: docs/README.md
  • files_exist - File is ignored: docs/usage.md
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File does not exist: CODE_OF_CONDUCT.md
  • 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 does not exist: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/feature_request.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-mikrokondo_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-mikrokondo_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-mikrokondo_logo_dark.png
  • files_unchanged - File does not exist: docs/README.md
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/mikrokondo/mikrokondo/.github/workflows/awstest.yml
  • multiqc_config - multiqc_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-30 20:18:30

@mattheww95 mattheww95 changed the base branch from main to dev July 25, 2024 17:07
@sgsutcliffe
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Included the override container registry process (for more information see phac-nml pipeline standards) to allow the container directives to have a conditional check in the nested ternary operator. Added this to the pilon_interactive process used in the module pilon_polisher.nfwhich uses docker.hub rather than the defaultquay.io`.

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Added the default container registries to quay.io 697cbb2

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sgsutcliffe commented Aug 30, 2024 •
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Resolving the branch conflict included updating the locidex container to the dockerhub repository. I'll add the same conditional operator to all the modules that use the params.locidex (i.e. locidex_extract.nf, locidex_search.nf, locidex_report.nf).

apetkau
apetkau requested changes Aug 30, 2024
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This looks great. Thanks so much for your work on this Steven and making all those changes/testing things out 😄

I just have one comment.

nextflow.config Outdated Show resolved Hide resolved
@mattheww95
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Just looked everything over! It looks great and thank you so much for your help!

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In addition to updating containers to use a default registry quay.io we will replace the python container.

    python3 {
        singularity = "biocontainers/staramr:0.10.0--pyhdfd78af_0"
        docker = "biocontainers/staramr:0.10.0--pyhdfd78af_0"
    }

Which has Python 3.11.4 running under the hood. So will replace with Python 3.12 (the closest quay.io container)

apetkau
apetkau approved these changes Aug 30, 2024
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Looks good. Thanks so much Steven 😄

@sgsutcliffe sgsutcliffe merged commit 380a1aa into dev Aug 30, 2024
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@sgsutcliffe sgsutcliffe deleted the patch/registries branch August 30, 2024 20:40
@mattheww95 mattheww95 mentioned this pull request Aug 30, 2024
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@apetkau apetkau apetkau approved these changes

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@mattheww95 @sgsutcliffe @apetkau