Harden schema validation error messages and docs by maxulysse · Pull Request #161 · nf-core/references

maxulysse · 2026-10-13T14:16:29Z

Summary

Implements the schema-hardening checklist from #107 (remaining PR 1 scope alongside #107/#101/#103):

nextflow_schema.json: errorMessage added to all pattern/range-bearing parameters (input, tools_bundle, tools, skip_tools, star_sjdbOverhang, star_genomeSAindexNbases, hisat2_build_memory); input mimetype fixed from text/csv to text/yaml; references_base_path given a real description and help text explaining the s3://ngi-igenomes/igenomes/ prefix rewrite; empty description/default leftovers removed from building_index_options.
schema_references.json: all 8 "errorMessage": "TODO" placeholders replaced with real messages (ASCAT fields, bed12, chr_dir, macs_gsize, mito_name).

Params coverage between main.nf and the schema verified in sync. No assets/schema_input.json exists — --input is validated via the schema keyword against schema_references.json, as intended.

Testing

Stub run: nextflow run . -profile test,docker --outdir /tmp/opencode/stub-results -stub — green (9 tasks)
tests/default.nf.test — green
prek run --all-files — green
Both schemas parse as valid JSON

Closes part of #107.

Generated by OpenCode

Add errorMessage coverage to nextflow_schema.json pattern-bearing parameters, fix the input mimetype to text/yaml, document references_base_path and its igenomes prefix-rewriting behaviour, and replace the eight placeholder TODO error messages in schema_references.json. Generated by OpenCode

github-actions · 2026-10-13T14:18:17Z

`nf-core pipelines lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 3e8a384

+| ✅ 216 tests passed       |+
#| ❔  12 tests were ignored |#
!| ❗   8 tests had warnings |!

Details

❗ Test warnings:

files_exist - File not found: .github/workflows/awsfulltest.yml
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 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 base.config: Check the defaults for all processes
pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/igenomes_ignored.config
files_exist - File is ignored: conf/test_full.config
nextflow_config - nextflow_config
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/nf-core-references_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-references_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-references_logo_dark.png
actions_awsfulltest - actions_awsfulltest
schema_params - schema_params

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/nf-test.yml
files_exist - File found: .github/actions/get-shards/action.yml
files_exist - File found: .github/actions/nf-test/action.yml
files_exist - File found: .github/workflows/pr-comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-references_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: docs/CONTRIBUTING.md
files_exist - File found: docs/images/nf-core-references_logo_light.png
files_exist - File found: docs/images/nf-core-references_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: nf-test.config
files_exist - File found: tests/default.nf.test
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: modules.json
files_exist - File found: ro-crate-metadata.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-references_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowReferences.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nf_test_content - 'tests/wbcel235.nf.test' contains outdir parameter
nf_test_content - 'tests/wbcel235.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/wbcel235.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/multiple.nf.test' contains outdir parameter
nf_test_content - 'tests/multiple.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/multiple.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/multiple.nf.test' contains outdir parameter
nf_test_content - 'tests/multiple.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/multiple.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/star.nf.test' contains outdir parameter
nf_test_content - 'tests/star.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/star.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/star.nf.test' contains outdir parameter
nf_test_content - 'tests/star.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/star.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/star.nf.test' contains outdir parameter
nf_test_content - 'tests/star.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/star.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/createsequencedictionary.nf.test' contains outdir parameter
nf_test_content - 'tests/createsequencedictionary.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/createsequencedictionary.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/snapaligner.nf.test' contains outdir parameter
nf_test_content - 'tests/snapaligner.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/snapaligner.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/salmon.nf.test' contains outdir parameter
nf_test_content - 'tests/salmon.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/salmon.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/salmon.nf.test' contains outdir parameter
nf_test_content - 'tests/salmon.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/salmon.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/hisat2.nf.test' contains outdir parameter
nf_test_content - 'tests/hisat2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/hisat2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/hisat2.nf.test' contains outdir parameter
nf_test_content - 'tests/hisat2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/hisat2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/hisat2.nf.test' contains outdir parameter
nf_test_content - 'tests/hisat2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/hisat2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/hisat2.nf.test' contains outdir parameter
nf_test_content - 'tests/sarek.nf.test' contains outdir parameter
nf_test_content - 'tests/sarek.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/sarek.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/sarek.nf.test' contains outdir parameter
nf_test_content - 'tests/sarek.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/sarek.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/kallisto.nf.test' contains outdir parameter
nf_test_content - 'tests/kallisto.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/kallisto.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/kallisto.nf.test' contains outdir parameter
nf_test_content - 'tests/kallisto.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/kallisto.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/samtools.nf.test' contains outdir parameter
nf_test_content - 'tests/samtools.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/samtools.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/samtools.nf.test' contains outdir parameter
nf_test_content - 'tests/samtools.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/samtools.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/samtools.nf.test' contains outdir parameter
nf_test_content - 'tests/samtools.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/samtools.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/rsem.nf.test' contains outdir parameter
nf_test_content - 'tests/rsem.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/rsem.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/rsem.nf.test' contains outdir parameter
nf_test_content - 'tests/rsem.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/rsem.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/htslib.nf.test' contains outdir parameter
nf_test_content - 'tests/htslib.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/htslib.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/htslib.nf.test' contains outdir parameter
nf_test_content - 'tests/htslib.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/htslib.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/default.nf.test' contains outdir parameter
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
nf_test_content - 'nf-test.config' sets a testsDir
nf_test_content - 'nf-test.config' sets a workDir
nf_test_content - 'nf-test.config' sets a configFile
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/workflows/pr-comment.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
actions_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
actions_nf_test - '.github/workflows/nf-test.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
readme - README Nextflow minimum version badge matched config. Badge: 26.04.0, Config: 26.04.0
readme - README nf-core template version badge found.
readme - README Zenodo placeholder was replaced with DOI.
pipeline_if_empty_null - No ifEmpty(null) strings found
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/yaml'
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: pr-comment.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - assets/multiqc_config.yml found and not ignored.
multiqc_config - assets/multiqc_config.yml contains report_section_order
multiqc_config - assets/multiqc_config.yml contains export_plots
multiqc_config - assets/multiqc_config.yml contains report_comment
multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
local_component_structure - local subworkflows directory structure is correct 'subworkflows/local/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - BUILD_INTERVALS found in conf/modules.config and Nextflow scripts.
modules_config - GFFREAD found in conf/modules.config and Nextflow scripts.
modules_config - KALLISTO_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - NCBIDATASETSCLI_DATASETS found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - RSEM_PREPAREREFERENCE_GENOME found in conf/modules.config and Nextflow scripts.
modules_config - STAR_GENOMEGENERATE found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 4.1.0
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.
container_configs - conf/containers_conda_lock_files_amd64.config is up to date
container_configs - conf/containers_conda_lock_files_arm64.config is up to date
container_configs - conf/containers_docker_amd64.config is up to date
container_configs - conf/containers_docker_arm64.config is up to date
container_configs - conf/containers_singularity_https_amd64.config is up to date
container_configs - conf/containers_singularity_https_arm64.config is up to date
container_configs - conf/containers_singularity_oras_amd64.config is up to date
container_configs - conf/containers_singularity_oras_arm64.config is up to date

Run details

nf-core/tools version 4.1.0
Run at 2026-10-13 14:42:30

Generated by OpenCode

github-actions · 2026-10-13T14:28:23Z

❌ 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 3/7

See the full run for details.

Generated by OpenCode

maxulysse added 2 commits October 13, 2026 16:24

Update changelog entries with PR number #161

b584818

Generated by OpenCode

Fix changelog link text for PR #161

c85497e

Generated by OpenCode

Clarify tools error messages and help text: no spaces in comma lists

3e8a384

Generated by OpenCode

maxulysse merged commit f935a44 into dev Oct 13, 2026
34 of 36 checks passed

maxulysse deleted the json-schema-improvements branch October 23, 2026 13:32

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Harden schema validation error messages and docs - #161

Harden schema validation error messages and docs#161
maxulysse merged 4 commits into
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json-schema-improvements

maxulysse commented Oct 13, 2026

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❗ Test warnings:

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maxulysse commented Oct 13, 2026

Summary

Testing

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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❌ nf-test failed with latest Nextflow version

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github-actions Bot commented Oct 13, 2026 •

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`nf-core pipelines lint` overall result: Passed ✅ ⚠️

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