Add conditional validation depending on the parameter type to the meta-schema

[fbdtemme]

Add conditional validation for all fields depending on the parameter type to the meta-schema.

Additionally this also checks for unevaluated properties to catch typos and wrong properties using the unevaluatedProperties feature.

The changes were tested on all nf-core pipelines:

Testing on all nf-core pipelines

Get the pipeline schema files:

wget https://nf-co.re/pipelines.json
cat pipelines.json | jq ".remote_workflows [].name" -r | xargs -I{} wget "https://raw.githubusercontent.com/nf-core/{}/master/nextflow_schema.json" -O {}_schema.json

Run the validation:

{ for f in *schema.json; do printf "# $f\n\n\`\`\`\n"; check-jsonschema --schemafile ../parameters_meta_schema.json $f; printf "\n\`\`\`\n\n"; done } | tee run.txt

Full output:

airrflow_schema.json

Schema validation errors were encountered.
  airrflow_schema.json::$.definitions.clonal_analysis_options.properties.clonal_threshold: Unevaluated properties are not allowed ('default', 'description', 'fa_icon', 'type' were unexpected)
  airrflow_schema.json::$.definitions.clonal_analysis_options.properties.clonal_threshold.type: ['string', 'number'] is not of type 'string'
  airrflow_schema.json::$.definitions.clonal_analysis_options.properties.clonal_threshold.type: ['string', 'number'] is not one of ['string', 'boolean', 'integer', 'number']

ampliseq_schema.json

Schema validation errors were encountered.
  ampliseq_schema.json::$.definitions.main_arguments.properties.input: Unevaluated properties are not allowed ('mimetype', 'schema' were unexpected)
  ampliseq_schema.json::$.definitions.main_arguments.properties.input_fasta: Unevaluated properties are not allowed ('mimetype' was unexpected)
  ampliseq_schema.json::$.definitions.main_arguments.properties.input_folder: Unevaluated properties are not allowed ('mimetype' was unexpected)

atacseq_schema.json

ok -- validation done

bacass_schema.json

Schema validation errors were encountered.
  bacass_schema.json::$.definitions.input_output_options.properties.input: Unevaluated properties are not allowed ('exist', 'mimetype', 'schema' were unexpected)
  bacass_schema.json::$.definitions.qc_and_trim.properties.save_trimmed_fail: Unevaluated properties are not allowed ('enum' was unexpected)

bactmap_schema.json

ok -- validation done

bamtofastq_schema.json

Schema validation errors were encountered.
  bamtofastq_schema.json::$.definitions.generic_options.properties.multiqc_logo: Unevaluated properties are not allowed ('exists' was unexpected)
  bamtofastq_schema.json::$.definitions.generic_options.properties.multiqc_methods_description: Unevaluated properties are not allowed ('exists' was unexpected)

cageseq_schema.json

Schema validation errors were encountered.
  cageseq_schema.json::$.definitions.alignment_options.properties.min_aln_length: Unevaluated properties are not allowed ('default' was unexpected)
  cageseq_schema.json::$.definitions.alignment_options.properties.min_aln_length.default: '15' is not of type 'integer', 'null'

callingcards_schema.json

ok -- validation done

chipseq_schema.json

ok -- validation done

circdna_schema.json

Schema validation errors were encountered.
  circdna_schema.json::$.definitions.amplicon_architect_options.properties.aa_data_repo: Unevaluated properties are not allowed ('mimetype' was unexpected)
  circdna_schema.json::$.definitions.amplicon_architect_options.properties.aa_cngain: Unevaluated properties are not allowed ('mimetype' was unexpected)
  circdna_schema.json::$.definitions.amplicon_architect_options.properties.mosek_license_dir: Unevaluated properties are not allowed ('mimetype' was unexpected)
  circdna_schema.json::$.definitions.amplicon_architect_options.properties.reference_build: Unevaluated properties are not allowed ('mimetype' was unexpected)
  circdna_schema.json::$.definitions.amplicon_architect_options.properties.cnvkit_cnn: Unevaluated properties are not allowed ('mimetype' was unexpected)

circrna_schema.json

Schema validation errors were encountered.
  circrna_schema.json::$.definitions.input_output_options.properties.input: Unevaluated properties are not allowed ('mimetype' was unexpected)
  circrna_schema.json::$.definitions.input_output_options.properties.phenotype: Unevaluated properties are not allowed ('mimetype' was unexpected)
  circrna_schema.json::$.definitions.pipeline_options.properties.module: Unevaluated properties are not allowed ('mandatory' was unexpected)
  circrna_schema.json::$.definitions.reference_genome_options.properties.gtf: Unevaluated properties are not allowed ('mimetype' was unexpected)
  circrna_schema.json::$.definitions.reference_genome_options.properties.mature: Unevaluated properties are not allowed ('mimetype' was unexpected)
  circrna_schema.json::$.definitions.generic_options.properties.email: Unevaluated properties are not allowed ('mimetype' was unexpected)

clipseq_schema.json

ok -- validation done

coproid_schema.json

ok -- validation done

createpanelrefs_schema.json

ok -- validation done

createtaxdb_schema.json

ok -- validation done

crisprseq_schema.json

ok -- validation done

crisprvar_schema.json

Several files failed to parse.
  Failed to parse crisprvar_schema.json

cutandrun_schema.json

ok -- validation done

ddamsproteomics_schema.json

Several files failed to parse.
  Failed to parse ddamsproteomics_schema.json

deepvariant_schema.json

Several files failed to parse.
  Failed to parse deepvariant_schema.json

demultiplex_schema.json

ok -- validation done

denovohybrid_schema.json

Several files failed to parse.
  Failed to parse denovohybrid_schema.json

detaxizer_schema.json

ok -- validation done

diaproteomics_schema.json

ok -- validation done

differentialabundance_schema.json

Schema validation errors were encountered.
  differentialabundance_schema.json::$.definitions.features_options.properties.features: Unevaluated properties are not allowed ('mimetype' was unexpected)

dualrnaseq_schema.json

Schema validation errors were encountered.
  dualrnaseq_schema.json::$.definitions.star_general.properties.limitBAMsortRAM: Unevaluated properties are not allowed ('default' was unexpected)
  dualrnaseq_schema.json::$.definitions.star_general.properties.limitBAMsortRAM.default: '0' is not of type 'integer', 'null'

eager_schema.json

Schema validation errors were encountered.
  eager_schema.json::$.definitions.mapping.properties.mapper: Unevaluated properties are not allowed ('title' was unexpected)

epitopeprediction_schema.json

ok -- validation done

exoseq_schema.json

Several files failed to parse.
  Failed to parse exoseq_schema.json

fastquorum_schema.json

ok -- validation done

fetchngs_schema.json

ok -- validation done

funcscan_schema.json

ok -- validation done

genomeannotator_schema.json

Several files failed to parse.
  Failed to parse genomeannotator_schema.json

genomeassembler_schema.json

ok -- validation done

genomeskim_schema.json

ok -- validation done

gwas_schema.json

ok -- validation done

hgtseq_schema.json

ok -- validation done

hicar_schema.json

ok -- validation done

hic_schema.json

Several files failed to parse.
  Failed to parse hic_schema.json

hlatyping_schema.json

ok -- validation done

imcyto_schema.json

Several files failed to parse.
  Failed to parse imcyto_schema.json

isoseq_schema.json

ok -- validation done

kmermaid_schema.json

Several files failed to parse.
  Failed to parse kmermaid_schema.json

liverctanalysis_schema.json

ok -- validation done

lncpipe_schema.json

Several files failed to parse.
  Failed to parse lncpipe_schema.json

mag_schema.json

Schema validation errors were encountered.
  mag_schema.json::$.definitions.quality_control_for_short_reads_options.properties.fastp_qualified_quality: Unevaluated properties are not allowed ('help' was unexpected)
  mag_schema.json::$.definitions.quality_control_for_short_reads_options.properties.fastp_cut_mean_quality: Unevaluated properties are not allowed ('help' was unexpected)

marsseq_schema.json

ok -- validation done

mcmicro_schema.json

ok -- validation done

metaboigniter_schema.json

ok -- validation done

metapep_schema.json

ok -- validation done

metatdenovo_schema.json

ok -- validation done

methylseq_schema.json

Schema validation errors were encountered.
  methylseq_schema.json::$.definitions.qualimap_options.properties.bamqc_regions_file: Unevaluated properties are not allowed ('description', 'help_text' were unexpected)
  methylseq_schema.json::$.definitions.qualimap_options.properties.bamqc_regions_file: 'type' is a required property

mhcquant_schema.json

Schema validation errors were encountered.
  mhcquant_schema.json::$.definitions.mass_spectrometry_data_processing.properties.annotate_ions: Unevaluated properties are not allowed ('default' was unexpected)
  mhcquant_schema.json::$.definitions.mass_spectrometry_data_processing.properties.annotate_ions.default: 'false' is not of type 'boolean', 'null'

mnaseseq_schema.json

Several files failed to parse.
  Failed to parse mnaseseq_schema.json

molkart_schema.json

ok -- validation done

multiplesequencealign_schema.json

ok -- validation done

nanoseq_schema.json

Schema validation errors were encountered.
  nanoseq_schema.json::$.definitions.input_output_options.properties.protocol: Unevaluated properties are not allowed ('format', 'mimetype', 'schema' were unexpected)
  nanoseq_schema.json::$.definitions.input_output_options.properties.protocol.format: 'sample-type' is not one of ['file-path', 'directory-path', 'path', 'file-path-pattern']

nanostring_schema.json

ok -- validation done

nascent_schema.json

ok -- validation done

neutronstar_schema.json

Several files failed to parse.
  Failed to parse neutronstar_schema.json

pangenome_schema.json

Schema validation errors were encountered.
  pangenome_schema.json::$.definitions.wfmash_options.properties.wfmash_sparse_map: Unevaluated properties are not allowed ('default' was unexpected)
  pangenome_schema.json::$.definitions.wfmash_options.properties.wfmash_sparse_map.default: '1.0' is not of type 'number', 'null'

pathogensurveillance_schema.json

ok -- validation done

pgdb_schema.json

ok -- validation done

phageannotator_schema.json

ok -- validation done

phyloplace_schema.json

ok -- validation done

pixelator_schema.json

Schema validation errors were encountered.
  pixelator_schema.json::$.definitions.adapterqc_options: 'type' is a required property
  pixelator_schema.json::$.definitions.demux_options: 'type' is a required property
  pixelator_schema.json::$.definitions.collapse_options: 'type' is a required property
  pixelator_schema.json::$.definitions.collapse_options.properties.markers_ignore: Unevaluated properties are not allowed ('fa-icon' was unexpected)
  pixelator_schema.json::$.definitions.graph_options: 'type' is a required property
  pixelator_schema.json::$.definitions.annotate_options: 'type' is a required property
  pixelator_schema.json::$.definitions.analysis_options: 'type' is a required property
  pixelator_schema.json::$.definitions.report_options: 'type' is a required property
  pixelator_schema.json::$.definitions.global_config_options.properties.pixelator_container: Unevaluated properties are not allowed ('format' was unexpected)
  pixelator_schema.json::$.definitions.global_config_options.properties.pixelator_container.format: 'url' is not one of ['file-path', 'directory-path', 'path', 'file-path-pattern']

proteinfold_schema.json

Schema validation errors were encountered.
  proteinfold_schema.json::$.definitions.colabfold_dbs_and_parameters_path_options.properties.colabfold_alphafold2_params_tags: Unevaluated properties are not allowed ('description', 'fa_icon', 'type' were unexpected)
  proteinfold_schema.json::$.definitions.colabfold_dbs_and_parameters_path_options.properties.colabfold_alphafold2_params_tags.type: 'object' is not one of ['string', 'boolean', 'integer', 'number']

proteomicslfq_schema.json

ok -- validation done

quantms_schema.json

Schema validation errors were encountered.
  quantms_schema.json::$.definitions.protein_quantification_dda.properties.ratios: Unevaluated properties are not allowed ('default' was unexpected)
  quantms_schema.json::$.definitions.protein_quantification_dda.properties.ratios.default: 'false' is not of type 'boolean', 'null'
  quantms_schema.json::$.definitions.protein_quantification_dda.properties.normalize: Unevaluated properties are not allowed ('default' was unexpected)
  quantms_schema.json::$.definitions.protein_quantification_dda.properties.normalize.default: 'false' is not of type 'boolean', 'null'
  quantms_schema.json::$.definitions.protein_quantification_dda.properties.fix_peptides: Unevaluated properties are not allowed ('default' was unexpected)
  quantms_schema.json::$.definitions.protein_quantification_dda.properties.fix_peptides.default: 'false' is not of type 'boolean', 'null'

radseq_schema.json

ok -- validation done

rangeland_schema.json

Schema validation errors were encountered.
  rangeland_schema.json::$.description: '' is too short
  rangeland_schema.json::$.definitions.input_output_options.properties.input: Unevaluated properties are not allowed ('mimetype' was unexpected)

raredisease_schema.json

Schema validation errors were encountered.
  raredisease_schema.json::$.definitions.reference_file_options.properties.bait_padding: Unevaluated properties are not allowed ('pattern' was unexpected)
  raredisease_schema.json::$.definitions.reference_file_options.properties.vcfanno_resources: Unevaluated properties are not allowed ('exists' was unexpected)
  raredisease_schema.json::$.definitions.reference_file_options.properties.vcfanno_toml: Unevaluated properties are not allowed ('exists' was unexpected)
  raredisease_schema.json::$.definitions.reference_file_options.properties.vcfanno_lua: Unevaluated properties are not allowed ('exists' was unexpected)
  raredisease_schema.json::$.definitions.reference_file_options.properties.vep_cache: Unevaluated properties are not allowed ('exists' was unexpected)

readsimulator_schema.json

ok -- validation done

riboseq_schema.json

Schema validation errors were encountered.
  riboseq_schema.json::$.definitions.reference_genome_options.properties.riboviz_index: Unevaluated properties are not allowed ('exists', 'format' were unexpected)
  riboseq_schema.json::$.definitions.reference_genome_options.properties.riboviz_index.format: 'dir-path' is not one of ['file-path', 'directory-path', 'path', 'file-path-pattern']
  riboseq_schema.json::$.definitions.Indexing.properties.build_indices: Unevaluated properties are not allowed ('default' was unexpected)
  riboseq_schema.json::$.definitions.Indexing.properties.build_indices.default: 'true' is not of type 'boolean', 'null'
  riboseq_schema.json::$.definitions.Trimming_options.properties.adapter_sequence: 'type' is a required property
  riboseq_schema.json::$.definitions.Trimming_options.properties.adapter_sequence.default: 'AGATCGGAAGAGCACACGTCTGAA' is not of type 'boolean', 'null'
  riboseq_schema.json::$.definitions.Trimming_options.properties.adapter_sequence.default: 'AGATCGGAAGAGCACACGTCTGAA' is not of type 'integer', 'null'
  riboseq_schema.json::$.definitions.Trimming_options.properties.adapter_sequence.default: 'AGATCGGAAGAGCACACGTCTGAA' is not of type 'number', 'null'
  riboseq_schema.json::$.definitions.Trimming_options.properties.single_end: Unevaluated properties are not allowed ('meta' was unexpected)

rnadnavar_schema.json

ok -- validation done

rnafusion_schema.json

ok -- validation done

rnaseq_schema.json

ok -- validation done

rnasplice_schema.json

ok -- validation done

rnavar_schema.json

ok -- validation done

sammyseq_schema.json

ok -- validation done

sarek_schema.json

ok -- validation done

scflow_schema.json

ok -- validation done

scrnaseq_schema.json

ok -- validation done

slamseq_schema.json

Several files failed to parse.
  Failed to parse slamseq_schema.json

smartseq2_schema.json

Several files failed to parse.
  Failed to parse smartseq2_schema.json

smrnaseq_schema.json

ok -- validation done

spatialtranscriptomics_schema.json

ok -- validation done

spinningjenny_schema.json

ok -- validation done

ssds_schema.json

ok -- validation done

taxprofiler_schema.json

Schema validation errors were encountered.
  taxprofiler_schema.json::$.definitions.preprocessing_general_qc_options.properties.skip_preprocessing_qc: Unevaluated properties are not allowed ('help' was unexpected)

variantcatalogue_schema.json

ok -- validation done

vipr_schema.json

Several files failed to parse.
  Failed to parse vipr_schema.json

viralintegration_schema.json

Schema validation errors were encountered.
  viralintegration_schema.json::$.definitions.input_output_options.properties.remove_duplicates: Unevaluated properties are not allowed ('default' was unexpected)
  viralintegration_schema.json::$.definitions.input_output_options.properties.remove_duplicates.default: 'true' is not of type 'boolean', 'null'

viralrecon_schema.json

ok -- validation done

The conditional validation catches some extra issues:

• mimetype and or schema being set without "format": "file-path".
• Unrecognised keys: mandatory (should be passed in required), help (should be help_text)
• Default values passed as strings instead of the actual type ('1.0' instead of 1.0)

This is a new PR moved from nf-validation: nextflow-io#146