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modify some ENA args - #122

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fix/center-name
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modify some ENA args#122
KateSakharova wants to merge 3 commits into
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fix/center-name

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@KateSakharova

@KateSakharova KateSakharova commented Oct 30, 2026 •
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Resolving #57

  • added optional --center_name to study registration script (we had it as well in assembly_uploader study_xml)
  • renamed centre_name to center_name where possible
  • added --submission-tool and --submission-tool-verison to STUDY xml (example in ENA from Maira https://www.ebi.ac.uk/ena/browser/api/xml/PRJEB75453)
  • added error message for --mode reads && --upload_tpa
  • added nf-test for genome_upload module

Ideally we should say "use --center-name in case of brokering". I'm not sure that genome_uploader would work if there would be no --center-name specified.

At the moment --center-name is kind of required because it is used in REGISTERSTUDY in all workflows. When genome_uploader will accept that argument as optional, we can add fix and notes about using that arg only for brokering

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github-actions Bot commented Oct 30, 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: 4.1.0.
Please update your pipeline to the latest version.

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

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github-actions Bot commented Oct 30, 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 1/7

See the full run for details.

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github-actions Bot commented Oct 30, 2026

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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 2dd7642

+| ✅ 259 tests passed       |+
#| ❔   9 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   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 fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 4.1.0
  • Run at 2026-10-30 22:54:22

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@KateSakharova