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Bugfix/submission alias clash#77

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timrozday-mgnify wants to merge 1 commit into
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bugfix/submission-alias-clash
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Bugfix/submission alias clash#77
timrozday-mgnify wants to merge 1 commit into
1.0.0from
bugfix/submission-alias-clash

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@timrozday-mgnify

@timrozday-mgnify timrozday-mgnify commented Jun 26, 2026

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Generate separate study_metadata.json files for each registerstudy test to avoid a submission alias clash which would result in ENA returning an error.

@timrozday-mgnify
Modify registerstudy tests to generate seperate study_metadata.json f…
6bfd1d7 
…iles for each test to avoid a submission alias clash
@timrozday-mgnify timrozday-mgnify changed the base branch from dev to 1.0.0 June 26, 2026 13:56
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github-actions Bot commented Jun 26, 2026

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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6bfd1d7

+| ✅ 252 tests passed       |+
#| ❔   8 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗  15 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 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 CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
  • 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
  • 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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
  • local_component_structure - genome_evaluation.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 2026-06-26 13:57:30

mberacochea
mberacochea reviewed Jun 26, 2026
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@mberacochea mberacochea left a comment

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The only change I would make is to use tmp file instead of a hardcoded path

Comment thread modules/local/registerstudy/tests/main.nf.test
@@ -1,3 +1,17 @@
def writeStudyMetadataJson = { String alias ->
def metadata = new File(System.getProperty("user.dir"), "modules/local/registerstudy/tests/study_metadata_${alias}.json")

@mberacochea mberacochea Jun 26, 2026

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I would use a tmp file instead

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@timrozday-mgnify @mberacochea