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Fixed some parameter schema types#144

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muffato merged 3 commits intodevfrom
schema_types
Feb 9, 2026
Merged

Fixed some parameter schema types#144
muffato merged 3 commits intodevfrom
schema_types

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@muffato muffato commented Feb 9, 2026

Fixed some file types in the nextflow parameter schema

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
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile 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).

Copilot AI review requested due to automatic review settings February 9, 2026 22:04
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github-actions bot commented Feb 9, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b684046

+| ✅ 167 tests passed       |+
#| ❔  26 tests were ignored |#
!| ❗  14 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: conf/igenomes_ignored.config
  • 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 main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • local_component_structure - pacbio_filter.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - input_merge.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - process_vcf.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - input_filter_split.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - filter_pacbio.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - deepvariant_caller.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - align_pacbio.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - convert_stats.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-variantcalling_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-variantcalling_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-variantcalling_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: assets/multiqc_config.yml
  • files_exist - File is ignored: conf/igenomes.config
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • nextflow_config - Config default ignored: params.vector_db
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: assets/nf-core-variantcalling_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-variantcalling_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-variantcalling_logo_dark.png
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/variantcalling/variantcalling/.github/workflows/awstest.yml
  • multiqc_config - multiqc_config

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.2
  • Run at 2026-02-09 22:14:36

Copilot AI reviewed Feb 9, 2026
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Pull request overview

This PR updates the Nextflow parameter JSON schema to correct/standardize parameter types/formats for file/path inputs so they validate properly with the nf-schema tooling used by the pipeline.

Changes:

  • Adjusts vector_db schema format.
  • Adds format: file-path and exists: true to several reference-related file parameters (fasta, fai, interval, include/exclude positions).
  • Updates several parameter descriptions alongside the schema tweaks.

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muffato and others added 2 commits February 9, 2026 22:12
@muffato
Fixed the grammar/spacing
6c8314f 
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
@muffato
typo
b684046 
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
@muffato muffato merged commit 1b0f1f9 into dev Feb 9, 2026
5 checks passed
@muffato muffato deleted the schema_types branch February 9, 2026 23:12
@muffato muffato added this to the v1.2.0 milestone Feb 19, 2026
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