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expected_inputs.json
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expected_inputs.json
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{
"immuno.vep_ensembl_species": "String",
"immuno.somaticExome.cnvkit_target_average_size": "Int? (optional)",
"immuno.pvacfuse_read_support": "Int? (optional)",
"immuno.examine_coding_effect": "Boolean (optional, default = true)",
"immuno.dna_sequencing_instrument": "String? (optional)",
"immuno.strelka_cpu_reserved": "Int (optional, default = 8)",
"immuno.manta_output_contigs": "Boolean? (optional)",
"immuno.gatk_haplotypecaller_intervals": "Array[Array[String]]",
"immuno.readcount_minimum_base_quality": "Int? (optional)",
"immuno.normal_cov": "Int? (optional)",
"immuno.trimming_max_uncalled": "Int",
"immuno.reference_dict": "File",
"immuno.peptide_fasta": "File? (optional)",
"immuno.target_interval_padding": "Int (optional, default = 100)",
"immuno.fasta_size": "Int? (optional)",
"immuno.optitype.threads": "Int (optional, default = 8)",
"immuno.vep_pick": "String? (optional)",
"immuno.hla_source_mode": "String",
"immuno.reference_bwt": "File",
"immuno.rna.unzip_fastqs": "Boolean (optional, default = true)",
"immuno.qc_minimum_mapping_quality": "Int (optional, default = 0)",
"immuno.rna_spike_in_error_rate": "String? (optional)",
"immuno.gene_transcript_lookup_table": "File",
"immuno.per_base_intervals": "Array[WomCompositeType {\n file -> File\nlabel -> String \n}]",
"immuno.tumor_sequence": "Array[WomCompositeType {\n sequence -> WomCompositeType {\n bam -> File?\nfastq1 -> File?\nfastq2 -> File? \n}\nreadgroup -> String? \n}]",
"immuno.docm_vcf_tbi": "File",
"immuno.ribosomal_intervals": "File",
"immuno.trimming_adapter_trim_end": "String",
"immuno.tumor_name": "String (optional, default = \"tumor\")",
"immuno.normal_dna_spike_in_error_rate": "String? (optional)",
"immuno.rna_annotation_file": "String? (optional)",
"immuno.percentile_threshold": "Int? (optional)",
"immuno.net_chop_threshold": "Float? (optional)",
"immuno.readcount_minimum_mapping_quality": "Int? (optional)",
"immuno.anchor_contribution_threshold": "Float? (optional)",
"immuno.clinical_mhc_classII_alleles": "Array[String]? (optional)",
"immuno.manta_call_regions_tbi": "File? (optional)",
"immuno.maximum_transcript_support_level": "Int? (optional)",
"immuno.validated_variants": "File? (optional)",
"immuno.min_ffpm_level": "Float? (optional, default = 0.05)",
"immuno.rna_sequencing_type": "String? (optional)",
"immuno.scatter_count": "Int (optional, default = 50)",
"immuno.vep_cache_dir_zip": "File",
"immuno.rna_sequencing_kit": "String? (optional)",
"immuno.run_reference_proteome_similarity": "Boolean? (optional)",
"immuno.exclude_nas": "Boolean? (optional)",
"immuno.reference_annotation": "File",
"immuno.reference": "File",
"immuno.dna_sequencing_platform": "String? (optional)",
"immuno.variants_to_table_fields": "Array[String] (optional, default = [\"CHROM\", \"POS\", \"ID\", \"REF\", \"ALT\", \"set\", \"AC\", \"AF\"])",
"immuno.normal_dna_total_dna": "String? (optional)",
"immuno.reference_0123": "File",
"immuno.reference_alt": "File",
"immuno.epitope_lengths_class_ii": "Array[Int]? (optional)",
"immuno.kallisto_index": "File",
"immuno.trimming_adapter_min_overlap": "Int",
"immuno.gvcf_gq_bands": "Array[String]",
"immuno.normal_sequence": "Array[WomCompositeType {\n sequence -> WomCompositeType {\n bam -> File?\nfastq1 -> File?\nfastq2 -> File? \n}\nreadgroup -> String? \n}]",
"immuno.netmhc_stab": "Boolean? (optional)",
"immuno.varscan_max_normal_freq": "Float? (optional)",
"immuno.rna_freq_normalization_method": "String? (optional)",
"immuno.vep_custom_annotations": "Array[WomCompositeType {\n force_report_coordinates -> Boolean\nmethod -> String\nannotation -> WomCompositeType {\n name -> String\ngnomad_filter -> Boolean?\ncheck_existing -> Boolean\nvcf_fields -> Array[String]?\ndata_format -> String\nfile -> File\nsecondary_files -> Array[File]? \n} \n}]",
"immuno.variants_to_table_genotype_fields": "Array[String] (optional, default = [\"GT\", \"AD\"])",
"immuno.refFlat": "File",
"immuno.strand": "String? (optional)",
"immuno.synonyms_file": "File? (optional)",
"immuno.tdna_vaf": "Float? (optional)",
"immuno.filter_docm_variants": "Boolean (optional, default = true)",
"immuno.iedb_retries": "Int? (optional)",
"immuno.rna_rin_score": "String? (optional)",
"immuno.pvacseq.expression_tool": "String (optional, default = \"kallisto\")",
"immuno.ploidy": "Int? (optional)",
"immuno.somaticExome.trimming": "WomCompositeType {\n adapters -> File\nmin_overlap -> Int \n}? (optional)",
"immuno.manta_non_wgs": "Boolean (optional, default = true)",
"immuno.net_chop_method": "String? (optional)",
"immuno.dna_sequencing_kit": "String? (optional)",
"immuno.vep_to_table_fields": "Array[String] (optional, default = [\"HGVSc\", \"HGVSp\"])",
"immuno.pvacfuse_keep_tmp_files": "Boolean? (optional)",
"immuno.reference_fai": "File",
"immuno.normal_name": "String (optional, default = \"normal\")",
"immuno.agfusion_annotate_noncanonical": "Boolean (optional, default = true)",
"immuno.varscan_strand_filter": "Int? (optional)",
"immuno.vep_ensembl_version": "String",
"immuno.somalier_vcf": "File",
"immuno.fp_min_var_freq": "Float? (optional)",
"immuno.trna_vaf": "Float? (optional)",
"immuno.sample_name": "String",
"immuno.trimming_adapters": "File",
"immuno.top_score_metric": "String? (optional)",
"immuno.rna_sequence": "Array[WomCompositeType {\n sequence -> WomCompositeType {\n bam -> File?\nfastq1 -> File?\nfastq2 -> File? \n}\nreadgroup -> String? \n}]",
"immuno.fusioninspector_mode": "String? (optional)",
"immuno.allele_specific_anchors": "Boolean? (optional)",
"immuno.bait_intervals": "File",
"immuno.manta_call_regions": "File? (optional)",
"immuno.normal_vaf": "Float? (optional)",
"immuno.annotate_coding_only": "Boolean (optional, default = false)",
"immuno.epitope_lengths_class_i": "Array[Int]? (optional)",
"immuno.per_target_intervals": "Array[WomCompositeType {\n file -> File\nlabel -> String \n}]",
"immuno.clinical_mhc_classI_alleles": "Array[String]? (optional)",
"immuno.tdna_cov": "Int? (optional)",
"immuno.qc_minimum_base_quality": "Int (optional, default = 0)",
"immuno.reference_genome_name": "String? (optional)",
"immuno.cdna_fasta": "File",
"immuno.additional_report_columns": "String? (optional)",
"immuno.phlat.mem": "Int (optional, default = 20)",
"immuno.dna_single_or_paired_end": "String? (optional)",
"immuno.bqsr_known_sites": "Array[File]",
"immuno.summary_intervals": "Array[WomCompositeType {\n file -> File\nlabel -> String \n}]",
"immuno.omni_vcf": "File",
"immuno.picard_metric_accumulation_level": "String",
"immuno.prediction_algorithms": "Array[String]",
"immuno.aggregate_inclusion_binding_threshold": "Int? (optional)",
"immuno.trimming_min_readlength": "Int",
"immuno.tumor_purity": "Float? (optional)",
"immuno.varscan_p_value": "Float? (optional)",
"immuno.filter_somatic_llr_tumor_purity": "Float? (optional)",
"immuno.problematic_amino_acids": "Array[String]? (optional)",
"immuno.target_intervals": "File",
"immuno.dna_sequencing_type": "String? (optional)",
"immuno.minimum_fold_change": "Float? (optional)",
"immuno.docm_vcf": "File",
"immuno.phlat.index_dir": "String (optional, default = \"\")",
"immuno.tumor_dna_total_dna": "String? (optional)",
"immuno.varscan_min_var_freq": "Float? (optional)",
"immuno.validated_variants_tbi": "File? (optional)",
"immuno.downstream_sequence_length": "Int? (optional)",
"immuno.normal_sample_name": "String",
"immuno.rna_sequencing_instrument": "String? (optional)",
"immuno.expn_val": "Float? (optional)",
"immuno.filter_gnomADe_maximum_population_allele_frequency": "Float? (optional)",
"immuno.binding_threshold": "Int? (optional)",
"immuno.optitype.mem": "Int (optional, default = 50)",
"immuno.rna_total_rna": "String? (optional)",
"immuno.trna_cov": "Int? (optional)",
"immuno.cle_vcf_filter": "Boolean (optional, default = false)",
"immuno.bqsr_known_sites_tbi": "Array[File]",
"immuno.reference_pac": "File",
"immuno.rna_sequencing_platform": "String? (optional)",
"immuno.reference_ann": "File",
"immuno.pvacseq_threads": "Int? (optional)",
"immuno.phlat.nthreads": "Int (optional, default = 8)",
"immuno.star_fusion_genome_dir_zip": "File",
"immuno.vep_ensembl_assembly": "String",
"immuno.filter_somatic_llr_normal_contamination_rate": "Float? (optional)",
"immuno.germline_filter_gnomAD_maximum_population_allele_frequency": "Float (optional, default = 1.1)",
"immuno.rna_single_or_paired_end": "String? (optional)",
"immuno.filter_somatic_llr_threshold": "Float? (optional)",
"immuno.tumor_sample_name": "String",
"immuno.gnomad_field_name": "String? (optional)",
"immuno.tumor_dna_spike_in_error_rate": "String? (optional)",
"immuno.allele_specific_binding_thresholds": "Boolean? (optional)",
"immuno.agfusion_database": "File",
"immuno.omni_vcf_tbi": "File",
"immuno.optitype_name": "String? (optional)",
"immuno.varscan_min_coverage": "Int? (optional)",
"immuno.reference_amb": "File",
"immuno.pvacfuse_expn_val": "Float? (optional)"
}