#/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow label: "Immunotherapy Workflow" requirements: - class: SchemaDefRequirement types: - $import: ../types/labelled_file.yml - $import: ../types/sequence_data.yml - class: SubworkflowFeatureRequirement inputs: #rnaseq inputs reference_index: type: File #this requires an extra file with the basename secondaryFiles: [".1.ht2", ".2.ht2", ".3.ht2", ".4.ht2", ".5.ht2", ".6.ht2", ".7.ht2", ".8.ht2"] reference_annotation: type: File rna_bams: type: File[] rna_readgroups: type: string[] read_group_fields: type: type: array items: type: array items: string sample_name: type: string trimming_adapters: type: File trimming_adapter_trim_end: type: string trimming_adapter_min_overlap: type: int trimming_max_uncalled: type: int trimming_min_readlength: type: int kallisto_index: type: File gene_transcript_lookup_table: type: File strand: type: - "null" - type: enum symbols: ["first", "second", "unstranded"] refFlat: type: File ribosomal_intervals: type: File reference_transcriptome: type: File #somatic inputs reference: string tumor_sequence: type: ../types/sequence_data.yml#sequence_data[] tumor_name: type: string? default: 'tumor' normal_sequence: type: ../types/sequence_data.yml#sequence_data[] normal_name: type: string? default: 'normal' mills: type: File secondaryFiles: [.tbi] known_indels: type: File secondaryFiles: [.tbi] dbsnp_vcf: type: File secondaryFiles: [.tbi] bqsr_intervals: type: string[] bait_intervals: type: File target_intervals: type: File per_base_intervals: type: ../types/labelled_file.yml#labelled_file[] per_target_intervals: type: ../types/labelled_file.yml#labelled_file[] summary_intervals: type: ../types/labelled_file.yml#labelled_file[] omni_vcf: type: File secondaryFiles: [.tbi] picard_metric_accumulation_level: type: string qc_minimum_mapping_quality: type: int? default: 0 qc_minimum_base_quality: type: int? default: 0 interval_list: type: File cosmic_vcf: type: File? secondaryFiles: [.tbi] panel_of_normals_vcf: type: File? secondaryFiles: [.tbi] strelka_cpu_reserved: type: int? default: 8 mutect_scatter_count: type: int mutect_artifact_detection_mode: type: boolean default: false mutect_max_alt_allele_in_normal_fraction: type: float? mutect_max_alt_alleles_in_normal_count: type: int? varscan_strand_filter: type: int? default: 0 varscan_min_coverage: type: int? default: 8 varscan_min_var_freq: type: float? default: 0.05 varscan_p_value: type: float? default: 0.99 varscan_max_normal_freq: type: float? pindel_insert_size: type: int default: 400 docm_vcf: type: File secondaryFiles: [.tbi] filter_docm_variants: type: boolean? default: true vep_cache_dir: type: string vep_ensembl_assembly: type: string doc: "genome assembly to use in vep. Examples: GRCh38 or GRCm38" vep_ensembl_version: type: string doc: "ensembl version - Must be present in the cache directory. Example: 95" vep_ensembl_species: type: string doc: "ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus" synonyms_file: type: File? annotate_coding_only: type: boolean? vep_pick: type: - "null" - type: enum symbols: ["pick", "flag_pick", "pick_allele", "per_gene", "pick_allele_gene", "flag_pick_allele", "flag_pick_allele_gene"] cle_vcf_filter: type: boolean default: false variants_to_table_fields: type: string[] default: [CHROM,POS,ID,REF,ALT,set,AC,AF] variants_to_table_genotype_fields: type: string[] default: [GT,AD] vep_to_table_fields: type: string[] default: [HGVSc,HGVSp] custom_gnomad_vcf: type: File? secondaryFiles: [.tbi] custom_clinvar_vcf: type: File? secondaryFiles: [.tbi] manta_call_regions: type: File? secondaryFiles: [.tbi] manta_non_wgs: type: boolean? default: true manta_output_contigs: type: boolean? somalier_vcf: type: File #germline inputs emit_reference_confidence: type: string gvcf_gq_bands: type: string[] gatk_haplotypecaller_intervals: type: type: array items: type: array items: string optitype_name: type: string? #phase_vcf inputs reference_dict: type: File #pvacseq inputs readcount_minimum_base_quality: type: int? readcount_minimum_mapping_quality: type: int? prediction_algorithms: type: string[] epitope_lengths: type: int[]? binding_threshold: type: int? allele_specific_binding_thresholds: type: boolean? minimum_fold_change: type: float? peptide_sequence_length: type: int? top_score_metric: type: - "null" - type: enum symbols: ["lowest", "median"] additional_report_columns: type: - "null" - type: enum symbols: ["sample_name"] fasta_size: type: int? downstream_sequence_length: type: string? exclude_nas: type: boolean? phased_proximal_variants_vcf: type: File? secondaryFiles: ['.tbi'] maximum_transcript_support_level: type: - "null" - type: enum symbols: ["1", "2", "3", "4", "5"] normal_cov: type: int? tdna_cov: type: int? trna_cov: type: int? normal_vaf: type: float? tdna_vaf: type: float? trna_vaf: type: float? expn_val: type: float? net_chop_method: type: - "null" - type: enum symbols: ["cterm", "20s"] net_chop_threshold: type: float? netmhc_stab: type: boolean? pvacseq_threads: type: int? immuno_tumor_sample_name: type: string immuno_normal_sample_name: type: string outputs: final_bam: type: File outputSource: rnaseq/final_bam secondaryFiles: [.bai] stringtie_transcript_gtf: type: File outputSource: rnaseq/stringtie_transcript_gtf stringtie_gene_expression_tsv: type: File outputSource: rnaseq/stringtie_gene_expression_tsv transcript_abundance_tsv: type: File outputSource: rnaseq/transcript_abundance_tsv transcript_abundance_h5: type: File outputSource: rnaseq/transcript_abundance_h5 gene_abundance: type: File outputSource: rnaseq/gene_abundance metrics: type: File outputSource: rnaseq/metrics chart: type: File outputSource: rnaseq/chart fusion_evidence: type: File outputSource: rnaseq/fusion_evidence unfiltered_fusion_seqs: type: File outputSource: rnaseq/unfiltered_fusion_seqs unfiltered_fusions_json: type: File outputSource: rnaseq/unfiltered_fusions_json filtered_fusion_seqs: type: File outputSource: rnaseq/filtered_fusion_seqs filtered_fusions_json: type: File outputSource: rnaseq/filtered_fusions_json final_fusion_calls: type: File outputSource: rnaseq/final_fusion_calls tumor_cram: type: File outputSource: somatic/tumor_cram tumor_mark_duplicates_metrics: type: File outputSource: somatic/tumor_mark_duplicates_metrics tumor_insert_size_metrics: type: File outputSource: somatic/tumor_insert_size_metrics tumor_alignment_summary_metrics: type: File outputSource: somatic/tumor_alignment_summary_metrics tumor_hs_metrics: type: File outputSource: somatic/tumor_hs_metrics tumor_per_target_coverage_metrics: type: File[] outputSource: somatic/tumor_per_target_coverage_metrics tumor_per_target_hs_metrics: type: File[] outputSource: somatic/tumor_per_target_hs_metrics tumor_per_base_coverage_metrics: type: File[] outputSource: somatic/tumor_per_base_coverage_metrics tumor_per_base_hs_metrics: type: File[] outputSource: somatic/tumor_per_base_hs_metrics tumor_summary_hs_metrics: type: File[] outputSource: somatic/tumor_summary_hs_metrics tumor_flagstats: type: File outputSource: somatic/tumor_flagstats tumor_verify_bam_id_metrics: type: File outputSource: somatic/tumor_verify_bam_id_metrics tumor_verify_bam_id_depth: type: File outputSource: somatic/tumor_verify_bam_id_depth normal_cram: type: File outputSource: somatic/normal_cram normal_mark_duplicates_metrics: type: File outputSource: somatic/normal_mark_duplicates_metrics normal_insert_size_metrics: type: File outputSource: somatic/normal_insert_size_metrics normal_alignment_summary_metrics: type: File outputSource: somatic/normal_alignment_summary_metrics normal_hs_metrics: type: File outputSource: somatic/normal_hs_metrics normal_per_target_coverage_metrics: type: File[] outputSource: somatic/normal_per_target_coverage_metrics normal_per_target_hs_metrics: type: File[] outputSource: somatic/normal_per_target_hs_metrics normal_per_base_coverage_metrics: type: File[] outputSource: somatic/normal_per_base_coverage_metrics normal_per_base_hs_metrics: type: File[] outputSource: somatic/normal_per_base_hs_metrics normal_summary_hs_metrics: type: File[] outputSource: somatic/normal_summary_hs_metrics normal_flagstats: type: File outputSource: somatic/normal_flagstats normal_verify_bam_id_metrics: type: File outputSource: somatic/normal_verify_bam_id_metrics normal_verify_bam_id_depth: type: File outputSource: somatic/normal_verify_bam_id_depth mutect_unfiltered_vcf: type: File outputSource: somatic/mutect_unfiltered_vcf secondaryFiles: [.tbi] mutect_filtered_vcf: type: File outputSource: somatic/mutect_filtered_vcf secondaryFiles: [.tbi] strelka_unfiltered_vcf: type: File outputSource: somatic/strelka_unfiltered_vcf secondaryFiles: [.tbi] strelka_filtered_vcf: type: File outputSource: somatic/strelka_filtered_vcf secondaryFiles: [.tbi] varscan_unfiltered_vcf: type: File outputSource: somatic/varscan_unfiltered_vcf secondaryFiles: [.tbi] varscan_filtered_vcf: type: File outputSource: somatic/varscan_filtered_vcf secondaryFiles: [.tbi] pindel_unfiltered_vcf: type: File outputSource: somatic/pindel_unfiltered_vcf secondaryFiles: [.tbi] pindel_filtered_vcf: type: File outputSource: somatic/pindel_filtered_vcf secondaryFiles: [.tbi] docm_filtered_vcf: type: File outputSource: somatic/docm_filtered_vcf secondaryFiles: [.tbi] somatic_final_vcf: type: File outputSource: somatic/final_vcf secondaryFiles: [.tbi] final_filtered_vcf: type: File outputSource: somatic/final_filtered_vcf secondaryFiles: [.tbi] final_tsv: type: File outputSource: somatic/final_tsv somatic_vep_summary: type: File outputSource: somatic/vep_summary tumor_snv_bam_readcount_tsv: type: File outputSource: somatic/tumor_snv_bam_readcount_tsv tumor_indel_bam_readcount_tsv: type: File outputSource: somatic/tumor_indel_bam_readcount_tsv normal_snv_bam_readcount_tsv: type: File outputSource: somatic/normal_snv_bam_readcount_tsv normal_indel_bam_readcount_tsv: type: File outputSource: somatic/normal_indel_bam_readcount_tsv intervals_antitarget: type: File? outputSource: somatic/intervals_antitarget intervals_target: type: File? outputSource: somatic/intervals_target normal_antitarget_coverage: type: File outputSource: somatic/normal_antitarget_coverage normal_target_coverage: type: File outputSource: somatic/normal_target_coverage reference_coverage: type: File? outputSource: somatic/reference_coverage cn_diagram: type: File? outputSource: somatic/cn_diagram cn_scatter_plot: type: File? outputSource: somatic/cn_scatter_plot tumor_antitarget_coverage: type: File outputSource: somatic/tumor_antitarget_coverage tumor_target_coverage: type: File outputSource: somatic/tumor_target_coverage tumor_bin_level_ratios: type: File outputSource: somatic/tumor_bin_level_ratios tumor_segmented_ratios: type: File outputSource: somatic/tumor_segmented_ratios diploid_variants: type: File? outputSource: somatic/diploid_variants secondaryFiles: [.tbi] somatic_variants: type: File? outputSource: somatic/somatic_variants secondaryFiles: [.tbi] all_candidates: type: File outputSource: somatic/all_candidates secondaryFiles: [.tbi] small_candidates: type: File outputSource: somatic/small_candidates secondaryFiles: [.tbi] tumor_only_variants: type: File? outputSource: somatic/tumor_only_variants secondaryFiles: [.tbi] somalier_concordance_metrics: type: File outputSource: somatic/somalier_concordance_metrics somalier_concordance_statistics: type: File outputSource: somatic/somalier_concordance_statistics cram: type: File outputSource: germline/cram mark_duplicates_metrics: type: File outputSource: germline/mark_duplicates_metrics insert_size_metrics: type: File outputSource: germline/insert_size_metrics insert_size_histogram: type: File outputSource: germline/insert_size_histogram alignment_summary_metrics: type: File outputSource: germline/alignment_summary_metrics hs_metrics: type: File outputSource: germline/hs_metrics per_target_coverage_metrics: type: File[] outputSource: germline/per_target_coverage_metrics per_target_hs_metrics: type: File[] outputSource: germline/per_target_hs_metrics per_base_coverage_metrics: type: File[] outputSource: germline/per_base_coverage_metrics per_base_hs_metrics: type: File[] outputSource: germline/per_base_hs_metrics summary_hs_metrics: type: File[] outputSource: germline/summary_hs_metrics flagstats: type: File outputSource: germline/flagstats verify_bam_id_metrics: type: File outputSource: germline/verify_bam_id_metrics verify_bam_id_depth: type: File outputSource: germline/verify_bam_id_depth gvcf: type: File[] outputSource: germline/gvcf germline_final_vcf: type: File outputSource: germline/final_vcf secondaryFiles: [.tbi] coding_vcf: type: File outputSource: germline/coding_vcf secondaryFiles: [.tbi] limited_vcf: type: File outputSource: germline/limited_vcf secondaryFiles: [.tbi] germline_vep_summary: type: File outputSource: germline/vep_summary optitype_tsv: type: File outputSource: germline/optitype_tsv optitype_plot: type: File outputSource: germline/optitype_plot phased_vcf: type: File outputSource: phase_vcf/phased_vcf secondaryFiles: [.tbi] allele_string: type: string[] outputSource: extract_alleles/allele_string annotated_vcf: type: File outputSource: pvacseq/annotated_vcf annotated_tsv: type: File outputSource: pvacseq/annotated_tsv mhc_i_all_epitopes: type: File? outputSource: pvacseq/mhc_i_all_epitopes mhc_i_filtered_epitopes: type: File? outputSource: pvacseq/mhc_i_filtered_epitopes mhc_i_ranked_epitopes: type: File? outputSource: pvacseq/mhc_i_ranked_epitopes mhc_ii_all_epitopes: type: File? outputSource: pvacseq/mhc_ii_all_epitopes mhc_ii_filtered_epitopes: type: File? outputSource: pvacseq/mhc_ii_filtered_epitopes mhc_ii_ranked_epitopes: type: File? outputSource: pvacseq/mhc_ii_ranked_epitopes combined_all_epitopes: type: File? outputSource: pvacseq/combined_all_epitopes combined_filtered_epitopes: type: File? outputSource: pvacseq/combined_filtered_epitopes combined_ranked_epitopes: type: File? outputSource: pvacseq/combined_ranked_epitopes steps: rnaseq: run: rnaseq.cwl in: reference_index: reference_index reference_annotation: reference_annotation instrument_data_bams: rna_bams read_group_id: rna_readgroups read_group_fields: read_group_fields sample_name: sample_name trimming_adapters: trimming_adapters trimming_adapter_trim_end: trimming_adapter_trim_end trimming_adapter_min_overlap: trimming_adapter_min_overlap trimming_max_uncalled: trimming_max_uncalled trimming_min_readlength: trimming_min_readlength kallisto_index: kallisto_index gene_transcript_lookup_table: gene_transcript_lookup_table strand: strand refFlat: refFlat ribosomal_intervals: ribosomal_intervals reference_transcriptome: reference_transcriptome species: vep_ensembl_species assembly: vep_ensembl_assembly out: [final_bam, stringtie_transcript_gtf, stringtie_gene_expression_tsv, transcript_abundance_tsv, transcript_abundance_h5, gene_abundance, metrics, chart, fusion_evidence, unfiltered_fusion_seqs, unfiltered_fusions_json, filtered_fusion_seqs, filtered_fusions_json, final_fusion_calls] somatic: run: somatic_exome.cwl in: reference: reference tumor_sequence: tumor_sequence tumor_name: tumor_name normal_sequence: normal_sequence normal_name: normal_name mills: mills known_indels: known_indels dbsnp_vcf: dbsnp_vcf bqsr_intervals: bqsr_intervals bait_intervals: bait_intervals target_intervals: target_intervals per_base_intervals: per_base_intervals per_target_intervals: per_target_intervals summary_intervals: summary_intervals omni_vcf: omni_vcf picard_metric_accumulation_level: picard_metric_accumulation_level qc_minimum_mapping_quality: qc_minimum_mapping_quality qc_minimum_base_quality: qc_minimum_base_quality interval_list: interval_list cosmic_vcf: cosmic_vcf panel_of_normals_vcf: panel_of_normals_vcf strelka_cpu_reserved: strelka_cpu_reserved mutect_scatter_count: mutect_scatter_count mutect_artifact_detection_mode: mutect_artifact_detection_mode mutect_max_alt_allele_in_normal_fraction: mutect_max_alt_allele_in_normal_fraction mutect_max_alt_alleles_in_normal_count: mutect_max_alt_alleles_in_normal_count varscan_strand_filter: varscan_strand_filter varscan_min_coverage: varscan_min_coverage varscan_min_var_freq: varscan_min_var_freq varscan_p_value: varscan_p_value varscan_max_normal_freq: varscan_max_normal_freq pindel_insert_size: pindel_insert_size docm_vcf: docm_vcf filter_docm_variants: filter_docm_variants vep_cache_dir: vep_cache_dir vep_ensembl_assembly: vep_ensembl_assembly vep_ensembl_version: vep_ensembl_version vep_ensembl_species: vep_ensembl_species synonyms_file: synonyms_file annotate_coding_only: annotate_coding_only vep_pick: vep_pick cle_vcf_filter: cle_vcf_filter variants_to_table_fields: variants_to_table_fields variants_to_table_genotype_fields: variants_to_table_genotype_fields vep_to_table_fields: vep_to_table_fields custom_gnomad_vcf: custom_gnomad_vcf custom_clinvar_vcf: custom_clinvar_vcf manta_call_regions: manta_call_regions manta_non_wgs: manta_non_wgs manta_output_contigs: manta_output_contigs somalier_vcf: somalier_vcf out: [tumor_cram,tumor_mark_duplicates_metrics,tumor_insert_size_metrics,tumor_alignment_summary_metrics,tumor_hs_metrics,tumor_per_target_coverage_metrics,tumor_per_target_hs_metrics,tumor_per_base_coverage_metrics,tumor_per_base_hs_metrics,tumor_summary_hs_metrics,tumor_flagstats,tumor_verify_bam_id_metrics,tumor_verify_bam_id_depth,normal_cram,normal_mark_duplicates_metrics,normal_insert_size_metrics,normal_alignment_summary_metrics,normal_hs_metrics,normal_per_target_coverage_metrics,normal_per_target_hs_metrics,normal_per_base_coverage_metrics,normal_per_base_hs_metrics,normal_summary_hs_metrics,normal_flagstats,normal_verify_bam_id_metrics,normal_verify_bam_id_depth,mutect_unfiltered_vcf,mutect_filtered_vcf,strelka_unfiltered_vcf,strelka_filtered_vcf,varscan_unfiltered_vcf,varscan_filtered_vcf,pindel_unfiltered_vcf,pindel_filtered_vcf,docm_filtered_vcf,final_vcf,final_filtered_vcf,final_tsv,vep_summary,tumor_snv_bam_readcount_tsv,tumor_indel_bam_readcount_tsv,normal_snv_bam_readcount_tsv,normal_indel_bam_readcount_tsv,intervals_antitarget,intervals_target,normal_antitarget_coverage,normal_target_coverage,reference_coverage,cn_diagram,cn_scatter_plot,tumor_antitarget_coverage,tumor_target_coverage,tumor_bin_level_ratios,tumor_segmented_ratios,diploid_variants,somatic_variants,all_candidates,small_candidates,tumor_only_variants,somalier_concordance_metrics,somalier_concordance_statistics] germline: run: germline_exome_hla_typing.cwl in: reference: reference sequence: normal_sequence mills: mills known_indels: known_indels dbsnp_vcf: dbsnp_vcf bqsr_intervals: bqsr_intervals bait_intervals: bait_intervals target_intervals: target_intervals per_base_intervals: per_base_intervals per_target_intervals: per_target_intervals summary_intervals: summary_intervals omni_vcf: omni_vcf picard_metric_accumulation_level: picard_metric_accumulation_level emit_reference_confidence: emit_reference_confidence gvcf_gq_bands: gvcf_gq_bands intervals: gatk_haplotypecaller_intervals vep_cache_dir: vep_cache_dir vep_ensembl_assembly: vep_ensembl_assembly vep_ensembl_version: vep_ensembl_version vep_ensembl_species: vep_ensembl_species synonyms_file: synonyms_file annotate_coding_only: annotate_coding_only custom_gnomad_vcf: custom_gnomad_vcf qc_minimum_mapping_quality: qc_minimum_mapping_quality qc_minimum_base_quality: qc_minimum_base_quality custom_clinvar_vcf: custom_clinvar_vcf optitype_name: optitype_name out: [cram,mark_duplicates_metrics,insert_size_metrics,insert_size_histogram,alignment_summary_metrics,hs_metrics,per_target_coverage_metrics,per_target_hs_metrics,per_base_coverage_metrics,per_base_hs_metrics,summary_hs_metrics,flagstats,verify_bam_id_metrics,verify_bam_id_depth,gvcf,final_vcf,coding_vcf,limited_vcf,vep_summary,optitype_tsv,optitype_plot] rename_somatic_vcf_tumor_sample: run: ../tools/replace_vcf_sample_name.cwl in: input_vcf: somatic/final_vcf sample_to_replace: default: 'TUMOR' new_sample_name: immuno_tumor_sample_name out: [renamed_vcf] rename_somatic_vcf_normal_sample: run: ../tools/replace_vcf_sample_name.cwl in: input_vcf: rename_somatic_vcf_tumor_sample/renamed_vcf sample_to_replace: default: 'NORMAL' new_sample_name: immuno_normal_sample_name out: [renamed_vcf] index_renamed_somatic: run: ../tools/index_vcf.cwl in: vcf: rename_somatic_vcf_normal_sample/renamed_vcf out: [indexed_vcf] phase_vcf: run: ../subworkflows/phase_vcf.cwl in: somatic_vcf: index_renamed_somatic/indexed_vcf germline_vcf: germline/final_vcf reference: reference reference_dict: reference_dict bam: somatic/tumor_cram normal_sample_name: immuno_normal_sample_name tumor_sample_name: immuno_tumor_sample_name out: [phased_vcf] extract_alleles: run: ../tools/extract_hla_alleles.cwl in: allele_file: germline/optitype_tsv out: [allele_string] pvacseq: run: ../subworkflows/pvacseq.cwl in: detect_variants_vcf: index_renamed_somatic/indexed_vcf sample_name: immuno_tumor_sample_name normal_sample_name: immuno_normal_sample_name rnaseq_bam: rnaseq/final_bam reference_fasta: reference readcount_minimum_base_quality: readcount_minimum_base_quality readcount_minimum_mapping_quality: readcount_minimum_mapping_quality gene_expression_file: rnaseq/gene_abundance transcript_expression_file: rnaseq/transcript_abundance_tsv alleles: extract_alleles/allele_string prediction_algorithms: prediction_algorithms epitope_lengths: epitope_lengths binding_threshold: binding_threshold allele_specific_binding_thresholds: allele_specific_binding_thresholds minimum_fold_change: minimum_fold_change peptide_sequence_length: peptide_sequence_length top_score_metric: top_score_metric additional_report_columns: additional_report_columns fasta_size: fasta_size downstream_sequence_length: downstream_sequence_length exclude_nas: exclude_nas phased_proximal_variants_vcf: phase_vcf/phased_vcf maximum_transcript_support_level: maximum_transcript_support_level normal_cov: normal_cov tdna_cov: tdna_cov trna_cov: trna_cov normal_vaf: normal_vaf tdna_vaf: tdna_vaf trna_vaf: trna_vaf expn_val: expn_val net_chop_method: net_chop_method net_chop_threshold: net_chop_threshold netmhc_stab: netmhc_stab n_threads: pvacseq_threads variants_to_table_fields: variants_to_table_fields variants_to_table_genotype_fields: variants_to_table_genotype_fields vep_to_table_fields: vep_to_table_fields out: [annotated_vcf, annotated_tsv, mhc_i_all_epitopes, mhc_i_filtered_epitopes, mhc_i_ranked_epitopes, mhc_ii_all_epitopes, mhc_ii_filtered_epitopes, mhc_ii_ranked_epitopes, combined_all_epitopes, combined_filtered_epitopes, combined_ranked_epitopes]