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Update public_aws_ecr.config #1048

Merged
merged 1 commit into from
Jun 15, 2023
Merged

Update public_aws_ecr.config #1048

merged 1 commit into from
Jun 15, 2023

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maxulysse
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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).

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github-actions bot commented Jun 14, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b94d105

+| ✅ 149 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • nextflow_config - Config manifest.version should end in dev: '3.12.0'
  • 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 2023-06-14 11:16:55

drpatelh
drpatelh reviewed Jun 15, 2023
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conf/public_aws_ecr.config
podman.registry = 'public.ecr.aws'
docker.registry = 'public.ecr.aws'
podman.registry = 'public.ecr.aws'
singularity.registry = 'public.ecr.aws'
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Will singularity ever be used on AWS in this context? To be fair, will podman ever be used either? Maybe having docker.registry is enough here?

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yes

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Without podman.registry podman will always fail because it will try to pull from docker.io/biocontainers/tool which doesn't exist. Same for singularity. Otherwise you will be using different versions of each tool with docker, podman and singularity.

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We had people trying to run singularity on AWS, so I'd rather be safe than sorry

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cf https://nfcore.slack.com/archives/CE6SDBX2A/p1686824156626549

@drpatelh drpatelh merged commit 9238ad2 into dev Jun 15, 2023
@drpatelh drpatelh deleted the maxulysse-patch-1 branch November 21, 2023 09:46
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@adamrtalbot adamrtalbot adamrtalbot approved these changes

@drpatelh drpatelh drpatelh left review comments

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@maxulysse @adamrtalbot @drpatelh