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fix: always skip igenomes_base validation#151

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fix/igenomes-base-validation
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fix: always skip igenomes_base validation#151
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fix/igenomes-base-validation

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@pinin4fjords

@pinin4fjords pinin4fjords commented Mar 6, 2026

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Summary

  • Always ignore igenomes_base during parameter validation
  • Remove format: directory-path from the igenomes_base schema definition

nf-schema 2.5.0+ validates cloud storage paths for format: directory-path parameters. Users without AWS credentials get validation failures (403 Access Denied) when nf-schema tries to check the S3 default path. Since igenomes_base is never used directly - derived reference paths are validated individually - we should always skip it.

This follows the nf-schema maintainer's recommendation in nextflow-io/nf-schema#204:

Having --igenomes_base as a default ignored parameter is the best solution here since all files derived from that path are validated themselves anyways.

Something I've also started doing is removing "format": "directory-path" and "exists": true from the igenomes base schema.

Same fix as nf-core/rnaseq#1745.

Test plan

  • Verify pipeline validates other parameters normally
  • Confirm runs without AWS credentials no longer fail on igenomes_base validation
  • Confirm igenomes_base is still functional when explicitly provided

🤖 Generated with Claude Code

pinin4fjords and others added 2 commits March 6, 2026 16:45
@pinin4fjords @claude
fix: always skip igenomes_base validation to prevent S3 access errors
f3816ed 
nf-schema 2.5.0+ validates cloud storage paths for format: directory-path
parameters. Users without AWS credentials get validation failures
(403 Access Denied) when nf-schema tries to check the S3 default path.
Since igenomes_base is never used directly and derived reference paths
are validated individually, always skip it per the nf-schema maintainer's
recommendation in nextflow-io/nf-schema#204.

Also removes format: directory-path from the schema for igenomes_base.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
@pinin4fjords @claude
docs: update changelog with PR #151
3fdad45 
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
@nf-core-bot

nf-core-bot commented Mar 6, 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: 3.5.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

@github-actions

github-actions Bot commented Mar 6, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3fdad45

+| ✅ 276 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   5 tests had warnings |!
Details

❗ Test warnings:

  • 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_if_empty_null - ifEmpty(null) found in /home/runner/work/riboseq/riboseq/subworkflows/local/prepare_genome/main.nf: _ versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
    _
  • schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.ribo_database_manifest
  • nf_test_content - nf_test_content
  • files_unchanged - File ignored due to lint config: assets/nf-core-riboseq_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-riboseq_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-riboseq_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-03-06 16:49:23

@pinin4fjords pinin4fjords enabled auto-merge March 6, 2026 17:21
@pinin4fjords pinin4fjords requested a review from maxulysse March 6, 2026 17:31
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