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Use the WEBIN from tester and stop hard-coding project accession during testing - #112

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ochkalova merged 6 commits into
nf-core:tests/any-credentialsfrom
aloraine:test/users-credentials
Oct 19, 2026
Merged

ochkalova merged 6 commits into
nf-core:tests/any-credentialsfrom
aloraine:test/users-credentials

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@aloraine

@aloraine aloraine commented Oct 16, 2026 •

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Closes #95

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/seqsubmit branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

@aloraine
aloraine requested a review from ochkalova October 16, 2026 10:53
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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 @aloraine,

It looks like this pull-request is has been made against the aloraine/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 aloraine/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!

@ochkalova
ochkalova changed the base branch from main to dev October 16, 2026 10:54
@github-actions

github-actions Bot commented Oct 16, 2026 •

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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a24634f

+| ✅ 251 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   4 tests had warnings |!
Details

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.0.0
  • 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

❔ 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 4.1.0
  • Run at 2026-10-16 13:48:16

@github-actions

github-actions Bot commented Oct 16, 2026 •

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❌ nf-test failed with latest Nextflow version

Note

Tests with Nextflow's latest version failed but it will not cause a CI workflow failure.
Please check if the failure is expected with newer (edge-)releases of Nextflow or if it needs fixing.

  • ❌ docker | latest-everything | Shard 6/7

See the full run for details.

@ochkalova ochkalova left a comment

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Thanks a lot Ann, once you decided to do all of them instead of just assembly with complete_metadata tests with and without fixed study, could you please also do the same renaming for mag test with complete_metadata

mag tests should also be done with and without fixed study

Comment on lines +6 to +8
"REGISTERSTUDY": {
"mgnify-pipelines-toolkit": "1.5.1"
},

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It shouldn't be there. That a bug described in #113
I'll fix it later, in the different branch

Comment on lines -67 to -79
"multiqc/multiqc_plots",
"multiqc/multiqc_plots/pdf",
"multiqc/multiqc_plots/pdf/Genomes assigned accessions.pdf",
"multiqc/multiqc_plots/pdf/genome_metadata.pdf",
"multiqc/multiqc_plots/pdf/sample_registration.pdf",
"multiqc/multiqc_plots/png",
"multiqc/multiqc_plots/png/Genomes assigned accessions.png",
"multiqc/multiqc_plots/png/genome_metadata.png",
"multiqc/multiqc_plots/png/sample_registration.png",
"multiqc/multiqc_plots/svg",
"multiqc/multiqc_plots/svg/Genomes assigned accessions.svg",
"multiqc/multiqc_plots/svg/genome_metadata.svg",
"multiqc/multiqc_plots/svg/sample_registration.svg",

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Those files are sopposed to be produced, I'll check it

Comment on lines +6 to +8
"REGISTERSTUDY": {
"mgnify-pipelines-toolkit": "1.5.1"
},

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It shouldn't be there. That a bug described in #113
I'll fix it later, in the different branch

@ochkalova
ochkalova changed the base branch from dev to tests/any-credentials October 19, 2026 11:21
@ochkalova
ochkalova merged commit 4ce0cc5 into nf-core:tests/any-credentials Oct 19, 2026
12 of 20 checks passed
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2 participants