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added env variables to AWS tests - #94

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fix/aws-tests
Draft

added env variables to AWS tests#94
KateSakharova wants to merge 1 commit into
mainfrom
fix/aws-tests

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@KateSakharova

@KateSakharova KateSakharova commented Aug 11, 2026

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@github-actions

github-actions Bot commented Aug 11, 2026

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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 @KateSakharova,

It looks like this pull-request is has been made against the nf-core/seqsubmit 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 nf-core/seqsubmit 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!

@github-actions

github-actions Bot commented Aug 11, 2026

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 4.0.3.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the Synchronisation documentation.

@github-actions

github-actions Bot commented Aug 11, 2026

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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c111f69

+| ✅ 253 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   4 tests had warnings |!
Details

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/seqsubmit/seqsubmit/lint_results.md: _* pipeline_if_empty_null - No ifEmpty(null) strings found
    _

❔ Tests ignored:

  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • files_exist - File is ignored: .github/workflows/linting_comment.yml
  • nextflow_config - Config variable ignored: params.input
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-seqsubmit_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-seqsubmit_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-seqsubmit_logo_dark.png
  • container_configs - container_configs

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.3
  • Run at 2026-08-11 14:39:50

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@KateSakharova