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Delete test files from the repo and use nf-core datasets instead#71

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ochkalova merged 3 commits into
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chores/move-test-data
Jun 10, 2026
Merged

Delete test files from the repo and use nf-core datasets instead#71
ochkalova merged 3 commits into
devfrom
chores/move-test-data

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@ochkalova

@ochkalova ochkalova commented Jun 10, 2026 •
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Resolves #48
Required to do before proper release.

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).

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github-actions Bot commented Jun 10, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 79174bb

+| ✅ 252 tests passed       |+
#| ❔   8 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗  14 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 README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • local_component_structure - genome_evaluation.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - rna_detection.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - fasta_validation.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • 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 4.0.2
  • Run at 2026-06-10 11:05:00

@ochkalova ochkalova force-pushed the chores/move-test-data branch from 462e83f to 12769af Compare June 10, 2026 11:02
@ochkalova ochkalova marked this pull request as ready for review June 10, 2026 11:07
ochkalova
ochkalova commented Jun 10, 2026
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Comment thread docs/usage.md
| `existing_study_type` | No | ENA study type (e.g. `Metagenomics`, `Other`). |
| `new_study_type` | No | Custom study type. Only used when `existing_study_type` is set to `Other`. |

An example metadata file is available at [assets/study_metadata.json](../assets/study_metadata.json).

@ochkalova ochkalova Jun 10, 2026

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There is an example above in the doc anyway, so I think it's fine to just remove this line

vagkaratzas
vagkaratzas approved these changes Jun 10, 2026
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@vagkaratzas vagkaratzas left a comment

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LGTM!

@ochkalova ochkalova merged commit b8cbf9b into dev Jun 10, 2026
22 checks passed
@ochkalova ochkalova deleted the chores/move-test-data branch June 10, 2026 11:17
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@vagkaratzas vagkaratzas vagkaratzas approved these changes

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Push all test data to nf-datasets

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@ochkalova @vagkaratzas