Parameters meta-schema - first draft

[ewels]

See nf-core/tools#2436

Still missing conditional validation - eg. that maxLength is only set when "type": "string"

[nvnieuwk]

😉

[ewels]

Testing on all nf-core pipelines...

Get the pipeline schema files:

wget https://nf-co.re/pipelines.json

for f in *for p in $(cat pipelines.json | jq ".remote_workflows [].name" -r)
do
wget "https://raw.githubusercontent.com/nf-core/${p}/master/nextflow_schema.json" -O ${p}_schema.json
done

Validate with check-jsonschema:

for f in *schema.json
do
printf "# $f\n\n"; check-jsonschema --schemafile ../parameters_meta_schema.json $f; printf "\n\n"
done

airrflow_schema.json

Schema validation errors were encountered.
  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']
  airrflow_schema.json::$.definitions.report_options.description: '' is too short

ampliseq_schema.json

Schema validation errors were encountered.
  ampliseq_schema.json::$.definitions.main_arguments.description: '' is too short
  ampliseq_schema.json::$.definitions.sequencing_input.description: '' is too short
  ampliseq_schema.json::$.definitions.read_trimming_and_quality_filtering.description: '' is too short
  ampliseq_schema.json::$.definitions.downstream_analysis.description: '' is too short
  ampliseq_schema.json::$.definitions.pipeline_report.description: '' is too short
  ampliseq_schema.json::$.definitions.skipping_specific_steps.description: '' is too short

atacseq_schema.json

ok -- validation done

bacass_schema.json

Schema validation errors were encountered.
  bacass_schema.json::$.definitions.contamination_screening.description: '' is too short
  bacass_schema.json::$.definitions.assembly_polishing.description: '' is too short
  bacass_schema.json::$.definitions.skipping_options.description: '' is too short

bactmap_schema.json

Schema validation errors were encountered.
  bactmap_schema.json::$.definitions.compulsory_parameters.description: '' is too short
  bactmap_schema.json::$.definitions.optional_pipeline_steps.description: '' is too short

bamtofastq_schema.json

ok -- validation done

cageseq_schema.json

ok -- validation done

callingcards_schema.json

Schema validation errors were encountered.
  callingcards_schema.json::$.definitions.alignment_options.description: '' is too short

chipseq_schema.json

ok -- validation done

circdna_schema.json

ok -- validation done

circrna_schema.json

ok -- validation done

clipseq_schema.json

ok -- validation done

coproid_schema.json

Schema validation errors were encountered.
  coproid_schema.json::$.definitions.pipeline_parameters.description: '' is too short

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

Schema validation errors were encountered.
  cutandrun_schema.json::$.definitions.flow_switching_options.description: '' is too short
  cutandrun_schema.json::$.definitions.trimming_options.description: '' is too short
  cutandrun_schema.json::$.definitions.pipeline_options.description: '' is too short
  cutandrun_schema.json::$.definitions.reporting_options.description: '' is too short

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

Schema validation errors were encountered.
  demultiplex_schema.json::$.definitions.workflow_options.description: '' is too short

denovohybrid_schema.json

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

detaxizer_schema.json

ok -- validation done

diaproteomics_schema.json

Schema validation errors were encountered.
  diaproteomics_schema.json::$.definitions.spectral_library_generation.description: '' is too short
  diaproteomics_schema.json::$.definitions.pseudo_irt_generation.description: '' is too short
  diaproteomics_schema.json::$.definitions.spectral_library_merging.description: '' is too short
  diaproteomics_schema.json::$.definitions.spectral_library_rt_alignment.description: '' is too short
  diaproteomics_schema.json::$.definitions.dia_spectral_library_search.description: '' is too short
  diaproteomics_schema.json::$.definitions.false_discovery_rate_estimation.description: '' is too short
  diaproteomics_schema.json::$.definitions.ms2_chromatogram_alignment.description: '' is too short
  diaproteomics_schema.json::$.definitions.output_summary.description: '' is too short

differentialabundance_schema.json

Schema validation errors were encountered.
  differentialabundance_schema.json::$.definitions.observations_options.description: '' is too short
  differentialabundance_schema.json::$.definitions.deseq2_specific_options_rna_seq_only.description: '' is too short
  differentialabundance_schema.json::$.definitions.limma_specific_options_microarray_only.description: '' is too short
  differentialabundance_schema.json::$.definitions.gsea.description: '' is too short
  differentialabundance_schema.json::$.definitions.shiny_app_settings.description: '' is too short
  differentialabundance_schema.json::$.definitions.reporting_options.description: '' is too short

dualrnaseq_schema.json

Schema validation errors were encountered.
  dualrnaseq_schema.json::$.definitions.star_salmon_alignment_based_mode.description: '' is too short
  dualrnaseq_schema.json::$.definitions.htseq_features.description: '' is too short
  dualrnaseq_schema.json::$.definitions.rna_mapping_statistics.description: '' is too short

eager_schema.json

ok -- validation done

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

Schema validation errors were encountered.
  hgtseq_schema.json::$.definitions.run_options.description: '' is too short

hic_schema.json

ok -- validation done

hicar_schema.json

ok -- validation done

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::$.definitions.input_output_options.properties.input.format: 'file-path-pattern' is not one of ['file-path', 'directory-path', 'path']
  mag_schema.json::$.definitions.quality_control_for_short_reads_options.description: '' is too short
  mag_schema.json::$.definitions.quality_control_for_long_reads_options.description: '' is too short
  mag_schema.json::$.definitions.taxonomic_profiling_options.properties.gtdbtk_min_completeness.minimum: 0.01 is not of type 'integer'
  mag_schema.json::$.definitions.assembly_options.description: '' is too short
  mag_schema.json::$.definitions.gene_prediction_and_annotation_options.description: '' is too short
  mag_schema.json::$.definitions.binning_options.description: '' is too short
  mag_schema.json::$.definitions.bin_quality_check_options.description: '' is too short

marsseq_schema.json

ok -- validation done

mcmicro_schema.json

ok -- validation done

metaboigniter_schema.json

Schema validation errors were encountered.
  metaboigniter_schema.json::$.definitions.internal_library_quantification_and_identification_parameters_negative_mode.properties.ipo_integrate_library_neg.help_text: '' is too short

metapep_schema.json

ok -- validation done

metatdenovo_schema.json

ok -- validation done

methylseq_schema.json

Schema validation errors were encountered.
  methylseq_schema.json::$.definitions.alignment_options.description: '' is too short
  methylseq_schema.json::$.definitions.bwa_meth_options.description: '' is too short
  methylseq_schema.json::$.definitions.qualimap_options.properties.bamqc_regions_file: 'type' is a required property
  methylseq_schema.json::$.definitions.skip_pipeline_steps.description: '' is too short

mhcquant_schema.json

Schema validation errors were encountered.
  mhcquant_schema.json::$.definitions.database_options.description: '' is too short
  mhcquant_schema.json::$.definitions.preprocessing.description: '' is too short
  mhcquant_schema.json::$.definitions.mass_spectrometry_data_processing.description: '' is too short
  mhcquant_schema.json::$.definitions.rescoring.description: '' is too short
  mhcquant_schema.json::$.definitions.quantification_options.description: '' is too short
  mhcquant_schema.json::$.definitions.mhc_affinity_prediction.description: '' is too short
  mhcquant_schema.json::$.definitions.variant_options.description: '' is too short

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.format: 'sample-type' is not one of ['file-path', 'directory-path', 'path']

nanostring_schema.json

ok -- validation done

nascent_schema.json

Schema validation errors were encountered.
  nascent_schema.json::$.definitions.alignment_options.description: '' is too short

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.seqwish_options.description: '' is too short

pathogensurveillance_schema.json

ok -- validation done

pgdb_schema.json

Schema validation errors were encountered.
  pgdb_schema.json::$.definitions.gnomad_variant_proteomes.description: '' is too short

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.adapterqc_options.properties.adapterqc_mismatches.maximum: 0.9 is not of type 'integer'
  pixelator_schema.json::$.definitions.demux_options: 'type' is a required property
  pixelator_schema.json::$.definitions.demux_options.properties.demux_mismatches.maximum: 0.9 is not of type 'integer'
  pixelator_schema.json::$.definitions.collapse_options: 'type' is a required property
  pixelator_schema.json::$.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.format: 'url' is not one of ['file-path', 'directory-path', 'path']

proteinfold_schema.json

Schema validation errors were encountered.
  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

Schema validation errors were encountered.
  proteomicslfq_schema.json::$.definitions.database_search.description: '' is too short
  proteomicslfq_schema.json::$.definitions.peptide_re_indexing.description: '' is too short
  proteomicslfq_schema.json::$.definitions.consensus_id.description: '' is too short
  proteomicslfq_schema.json::$.definitions.protein_quantification.description: '' is too short
  proteomicslfq_schema.json::$.definitions.statistical_post_processing.description: '' is too short
  proteomicslfq_schema.json::$.definitions.quality_control.description: '' is too short

quantms_schema.json

Schema validation errors were encountered.
  quantms_schema.json::$.definitions.database_search.description: '' is too short
  quantms_schema.json::$.definitions.peptide_re_indexing.description: '' is too short
  quantms_schema.json::$.definitions.consensus_id.description: '' is too short
  quantms_schema.json::$.definitions.protein_quantification_lfq.description: '' is too short
  quantms_schema.json::$.definitions.statistical_post_processing.description: '' is too short
  quantms_schema.json::$.definitions.quality_control.description: '' is too short

radseq_schema.json

ok -- validation done

raredisease_schema.json

ok -- validation done

readsimulator_schema.json

ok -- validation done

riboseq_schema.json

Schema validation errors were encountered.
  riboseq_schema.json::$.definitions.reference_genome_options.properties.riboviz_index.format: 'dir-path' is not one of ['file-path', 'directory-path', 'path']
  riboseq_schema.json::$.definitions.Trimming_options.properties.adapter_sequence: 'type' is a required property

rnadnavar_schema.json

ok -- validation done

rnafusion_schema.json

ok -- validation done

rnaseq_schema.json

ok -- validation done

rnasplice_schema.json

Schema validation errors were encountered.
  rnasplice_schema.json::$.definitions.dexseq_deu_options.description: '' is too short
  rnasplice_schema.json::$.definitions.edger_deu_options.description: '' is too short
  rnasplice_schema.json::$.definitions.dexseq_dtu_options.description: '' is too short
  rnasplice_schema.json::$.definitions.miso.description: '' is too short
  rnasplice_schema.json::$.definitions.suppa_options.description: '' is too short

rnavar_schema.json

Schema validation errors were encountered.
  rnavar_schema.json::$.definitions.preprocessing.description: '' is too short
  rnavar_schema.json::$.definitions.variant_calling.description: '' is too short
  rnavar_schema.json::$.definitions.variant_annotation.description: '' is too short

sammyseq_schema.json

ok -- validation done

sarek_schema.json

Schema validation errors were encountered.
  sarek_schema.json::$.definitions.annotation.description: '' is too short

scflow_schema.json

ok -- validation done

scrnaseq_schema.json

Schema validation errors were encountered.
  scrnaseq_schema.json::$.definitions.mandatory_arguments.description: '' is too short
  scrnaseq_schema.json::$.definitions.alevin_options.description: '' is too short
  scrnaseq_schema.json::$.definitions.starsolo_options.description: '' is too short

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::$.definitions.profiling_options.description: '' is too short
  taxprofiler_schema.json::$.definitions.postprocessing_and_visualisation_options.description: '' is too short

variantcatalogue_schema.json

ok -- validation done

vipr_schema.json

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

viralintegration_schema.json

ok -- validation done

viralrecon_schema.json

ok -- validation done

[ewels]

Almost all current validation errors are due to empty description strings...

[ewels]

I think this is going to be quite useful! If allowing empty description strings, these are the errors that we're left with - basically all look like unintentional errors in schema:

airrflow

Schema validation errors were encountered.
  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']

Yup, can't have an array for type, this is invalid:

"properties": {
    "clonal_threshold": {
        "type": ["string", "number"],

mag

Schema validation errors were encountered.
  mag_schema.json::$.definitions.taxonomic_profiling_options.properties.gtdbtk_min_completeness.minimum: 0.01 is not of type 'integer'

metaboigniter

Schema validation errors were encountered.
  metaboigniter_schema.json::$.definitions.internal_library_quantification_and_identification_parameters_negative_mode.properties.ipo_integrate_library_neg.help_text: '' is too short

methylseq

Schema validation errors were encountered.
  methylseq_schema.json::$.definitions.qualimap_options.properties.bamqc_regions_file: 'type' is a required property

nanoseq

Schema validation errors were encountered.
  nanoseq_schema.json::$.definitions.input_output_options.properties.protocol.format: 'sample-type' is not one of ['file-path', 'directory-path', 'path']

pixelator

Schema validation errors were encountered.
  pixelator_schema.json::$.definitions.adapterqc_options: 'type' is a required property
  pixelator_schema.json::$.definitions.adapterqc_options.properties.adapterqc_mismatches.maximum: 0.9 is not of type 'integer'
  pixelator_schema.json::$.definitions.demux_options: 'type' is a required property
  pixelator_schema.json::$.definitions.demux_options.properties.demux_mismatches.maximum: 0.9 is not of type 'integer'
  pixelator_schema.json::$.definitions.collapse_options: 'type' is a required property
  pixelator_schema.json::$.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.format: 'url' is not one of ['file-path', 'directory-path', 'path']

proteinfold

Schema validation errors were encountered.
  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']

This is valid JSON-schema, but not officially supported by the Nextflow schema stack:

"colabfold_alphafold2_params_tags": {
    "type": "object",
    "description": "Dictionary with Alphafold2 parameters tags",

riboseq

Schema validation errors were encountered.
  riboseq_schema.json::$.definitions.reference_genome_options.properties.riboviz_index.format: 'dir-path' is not one of ['file-path', 'directory-path', 'path']
  riboseq_schema.json::$.definitions.Trimming_options.properties.adapter_sequence: 'type' is a required property

[ewels]

I've removed the zero-length description thing, as this schema is intended to validate that Nextflow schema files are valid on a functional level. We should build best-practice linting for this kind of thing into nf-core/tools separately.

It may be worth removing the > zero-length string requirement for help_text too 🤔 Though that one isn't triggering any errors for nf-core pipelines (presumably due to difference in underlying schema-builder tool stack) so it's not so important.

[mashehu]

how about adding a description with a link to fontaweseome?

[ewels]

Description is a Nextflow schema thing, not a JSON schema thing (it's a non-standard field).

We already document it here: https://nextflow-io.github.io/nf-validation/nextflow_schema/nextflow_schema_specification/#fa_icon

[mirpedrol]

LGTM