{"@id":"https://w3id.org/cwl/view/git/038cb3617a1966a1057386adcde97ce55d9e1139/definitions/pipelines/immuno.cwl","retrievedFrom":{"repoUrl":"https://github.com/genome/analysis-workflows.git","branch":"038cb3617a1966a1057386adcde97ce55d9e1139","path":"definitions/pipelines/immuno.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/genome/analysis-workflows/038cb3617a1966a1057386adcde97ce55d9e1139/definitions/pipelines/immuno.cwl","url":"https://github.com/genome/analysis-workflows/blob/038cb3617a1966a1057386adcde97ce55d9e1139/definitions/pipelines/immuno.cwl"},"retrievedOn":"2026-08-28T05:56:55.769+00:00","lastCommit":"038cb3617a1966a1057386adcde97ce55d9e1139","label":"Immunotherapy Workflow","inputs":{"mills":{"label":"mills: File specifying common polymorphic indels from mills et al.","doc":"mills provides known polymorphic indels recommended by GATK for a variety of\ntools including the BaseRecalibrator. This file is part of the GATK resource\nbundle available at http://www.broadinstitute.org/gatk/guide/article?id=1213\nEssentially it is a list of known indels originally discovered by mill et al.\nhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC1557762/\nFile should be in vcf format, and tabix indexed.\n","type":"File"},"strand":{},"refFlat":{"type":"File"},"docm_vcf":{"type":"File"},"expn_val":{"type":"Float (Optional)"},"omni_vcf":{"type":"File"},"rna_bams":{"type":"File[]"},"tdna_cov":{"type":"Integer (Optional)"},"tdna_vaf":{"type":"Float (Optional)"},"trna_cov":{"type":"Integer (Optional)"},"trna_vaf":{"type":"Float (Optional)"},"vep_pick":{},"dbsnp_vcf":{"label":"dbsnp_vcf: File specifying common polymorphic indels from dbSNP","doc":"dbsnp_vcf provides known indels reecommended by GATK for a variety of tools\nincluding the BaseRecalibrator. This file is part of the GATK resource bundle\navailable at http://www.broadinstitute.org/gatk/guide/article?id=1213\nEssintially it is a list of known indels from dbSNP. File should be in vcf format,\nand tabix indexed.\n","type":"File"},"reference":{"label":"reference: Reference fasta file for a desired assembly","doc":"reference contains the nucleotide sequence for a given assembly (hg37, hg38, etc.)\nin fasta format for the entire genome. This is what reads will be aligned to.\nAppropriate files can be found on ensembl at https://ensembl.org/info/data/ftp/index.html\nWhen providing the reference secondary files corresponding to reference indices must be\nlocated in the same directory as the reference itself. These files can be created with\nsamtools index, bwa index, and picard CreateSequenceDictionary.\n","type":"File"},"cosmic_vcf":{"type":"File (Optional)"},"fasta_size":{"type":"Integer (Optional)"},"normal_cov":{"type":"Integer (Optional)"},"normal_vaf":{"type":"Float (Optional)"},"tumor_name":{"label":"tumor_name: String specifying the name of the MT sample","doc":"tumor_name provides a string for what the MT sample will be referred to in the various\noutputs, for exmaple the VCF files.\n","type":"String (Optional)"},"exclude_nas":{"type":"Boolean (Optional)"},"netmhc_stab":{"label":"netmhc_stab: sets an option whether to run  NetMHCStabPan or not","doc":"netmhc_stab sets an option that decides whether it will run NetMHCStabPan after all filtering and add stability predictions to predicted epitopes.\n","type":"Boolean (Optional)"},"normal_name":{"label":"normal_name: String specifying the name of the WT sample","doc":"normal_name provides a string for what the WT sample will be referred to in the various\noutputs, for exmaple the VCF files.\n","type":"String (Optional)"},"sample_name":{"type":"String"},"known_indels":{"label":"known_indels: File specifying common polymorphic indels from 1000G","doc":"known_indels provides known indels reecommended by GATK for a variety of tools\nincluding the BaseRecalibrator. This file is part of the GATK resource bundle\navailable at http://www.broadinstitute.org/gatk/guide/article?id=1213\nEssintially it is a list of known indels from 1000 Genomes Phase I indel calls.\nFile should be in vcf format, and tabix indexed.\n","type":"File"},"somalier_vcf":{"type":"File"},"gvcf_gq_bands":{"type":"String[]"},"interval_list":{"type":"File"},"manta_non_wgs":{"type":"Boolean (Optional)"},"optitype_name":{"type":"String (Optional)"},"synonyms_file":{"type":"File (Optional)"},"vep_cache_dir":{"type":"Directory"},"bait_intervals":{"label":"bait_intervals: interval_list file of baits used in the sequencing experiment","doc":"bait_intervals is an interval_list corresponding to the baits used in sequencing reagent.\nThese are essentially coordinates for regions you were able to design probes for in the reagent.\nTypically the reagent provider has this information available in bed format and it can be\nconverted to an interval_list with Picards BedToIntervalList. AstraZeneca also maintains a repo\nof baits for common sequencing reagents available at https://github.com/AstraZeneca-NGS/reference_data\n","type":"File"},"bqsr_intervals":{"label":"bqsr_intervals: Array of strings specifying regions for base quality score recalibration","doc":"bqsr_intervals provides an array of genomic intervals for which to apply\nGATK base quality score recalibrations. Typically intervals are given\nfor the entire chromosome (i.e. chr1, chr2, etc.), these names should match\nthe format in the reference file.\n","type":"String[]"},"cle_vcf_filter":{"type":"Boolean"},"kallisto_index":{"type":"File"},"known_variants":{"doc":"Previously discovered variants to be flagged in this pipelines's output vcf","type":"File (Optional)"},"reference_dict":{"type":"File"},"rna_readgroups":{"type":"String[]"},"tumor_sequence":{"label":"tumor_sequence: file specifying the location of MT sequencing data","doc":"tumor_sequence is a data structure described in sequence_data.yml used to pass information regarding\nsequencing data for single sample (i.e. fastq files). If more than one fastq file exist\nfor a sample, as in the case for multiple instrument data, the sequence tag is simply\nrepeated with the additional data (see example input file). Note that in the @RG field\nID and SM are required.\n","type":"https://w3id.org/cwl/view/git/038cb3617a1966a1057386adcde97ce55d9e1139/definitions/types/sequence_data.yml#sequence_data[]"},"epitope_lengths":{"type":"Integer[] (Optional)"},"net_chop_method":{"label":"net_chop_method: NetChop prediction method to use ('cterm' for C term 3.0, '20s' for 20S 3.0)","doc":"net_chop_method is used to specify which NetChop prediction method to use (\\\"cterm\\\" for C term 3.0, \\\"20s\\\" for 20S 3.0).\nC-term 3.0 is trained with publicly available MHC class I ligands and the authors believe that is performs best in predicting the\nboundaries of CTL epitopes. 20S is trained with in vitro degradation data.\n"},"normal_sequence":{"label":"normal_sequence: file specifying the location of WT sequencing data","doc":"normal_sequence is a data structure described in sequence_data.yml used to pass information regarding\nsequencing data for single sample (i.e. fastq files). If more than one fastq file exist\nfor a sample, as in the case for multiple instrument data, the sequence tag is simply\nrepeated with the additional data (see example input file). Note that in the @RG field\nID and SM are required.\n","type":"https://w3id.org/cwl/view/git/038cb3617a1966a1057386adcde97ce55d9e1139/definitions/types/sequence_data.yml#sequence_data[]"},"pvacseq_threads":{"label":"pvacseq_threads: Number of threads to use for parallelizing pvacseq prediction","doc":"pvacseq_threads specifies the number of threads to use for parallelizing peptide-MHC binding prediction calls.\n","type":"Integer (Optional)"},"reference_index":{"type":"File"},"varscan_p_value":{"type":"Float (Optional)"},"target_intervals":{"label":"target_intervals: interval_list file of targets used in the sequencing experiment","doc":"target_intervals is an interval_list corresponding to the targets for the sequencing reagent.\nThese are essentially coordinates for regions you wanted to design probes for in the reagent.\nBed files with this information can be converted to interval_lists with Picards BedToIntervalList.\nIn general for a WES exome reagent bait_intervals and target_intervals are the same.\n","type":"File"},"top_score_metric":{},"binding_threshold":{"type":"Integer (Optional)"},"read_group_fields":{"type":"bb01bc4cf68f247ed527840cd58121a0[]"},"summary_intervals":{"type":"https://w3id.org/cwl/view/git/038cb3617a1966a1057386adcde97ce55d9e1139/definitions/types/labelled_file.yml#labelled_file[]"},"trimming_adapters":{"type":"File"},"tumor_sample_name":{"label":"tumor_sample_name: Name of the tumor sample","doc":"tumor_sample_name is the name of the tumor sample being processed. 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file specifying the location of WT sequencing data\"];\n    \"net_chop_threshold\" [fillcolor=\"#94DDF4\",label=\"net_chop_threshold: NetChop prediction threshold\"];\n    \"trna_vaf\" [fillcolor=\"#94DDF4\",label=\"trna_vaf\"];\n    \"vep_ensembl_version\" [fillcolor=\"#94DDF4\",label=\"vep_ensembl_version\"];\n    \"strelka_cpu_reserved\" [fillcolor=\"#94DDF4\",label=\"strelka_cpu_reserved\"];\n    \"emit_reference_confidence\" [fillcolor=\"#94DDF4\",label=\"emit_reference_confidence\"];\n    \"ribosomal_intervals\" [fillcolor=\"#94DDF4\",label=\"ribosomal_intervals\"];\n    \"peptide_sequence_length\" [fillcolor=\"#94DDF4\",label=\"peptide_sequence_length\"];\n    \"varscan_strand_filter\" [fillcolor=\"#94DDF4\",label=\"varscan_strand_filter\"];\n    \"target_intervals\" [fillcolor=\"#94DDF4\",label=\"target_intervals: interval_list file of targets used in the sequencing experiment\"];\n    \"phased_proximal_variants_vcf\" [fillcolor=\"#94DDF4\",label=\"phased_proximal_variants_vcf\"];\n    \"qc_minimum_base_quality\" [fillcolor=\"#94DDF4\",label=\"qc_minimum_base_quality\"];\n    \"manta_non_wgs\" [fillcolor=\"#94DDF4\",label=\"manta_non_wgs\"];\n    \"panel_of_normals_vcf\" [fillcolor=\"#94DDF4\",label=\"panel_of_normals_vcf\"];\n    \"readcount_minimum_base_quality\" [fillcolor=\"#94DDF4\",label=\"readcount_minimum_base_quality\"];\n    \"variants_to_table_fields\" [fillcolor=\"#94DDF4\",label=\"variants_to_table_fields\"];\n    \"manta_output_contigs\" [fillcolor=\"#94DDF4\",label=\"manta_output_contigs\"];\n    \"known_variants\" [fillcolor=\"#94DDF4\",label=\"known_variants\"];\n    \"tdna_cov\" [fillcolor=\"#94DDF4\",label=\"tdna_cov\"];\n    \"cle_vcf_filter\" [fillcolor=\"#94DDF4\",label=\"cle_vcf_filter\"];\n    \"reference_annotation\" [fillcolor=\"#94DDF4\",label=\"reference_annotation\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"cram\" [fillcolor=\"#94DDF4\",label=\"cram\"];\n    \"annotated_vcf\" [fillcolor=\"#94DDF4\",label=\"annotated_vcf\"];\n    \"intervals_antitarget\" [fillcolor=\"#94DDF4\",label=\"intervals_antitarget\"];\n    \"somatic_vep_summary\" [fillcolor=\"#94DDF4\",label=\"somatic_vep_summary\"];\n    \"transcript_abundance_tsv\" [fillcolor=\"#94DDF4\",label=\"transcript_abundance_tsv\"];\n    \"tumor_cram\" [fillcolor=\"#94DDF4\",label=\"tumor_cram\"];\n    \"strelka_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"strelka_filtered_vcf\"];\n    \"tumor_flagstats\" [fillcolor=\"#94DDF4\",label=\"tumor_flagstats\"];\n    \"tumor_indel_bam_readcount_tsv\" [fillcolor=\"#94DDF4\",label=\"tumor_indel_bam_readcount_tsv\"];\n    \"normal_snv_bam_readcount_tsv\" [fillcolor=\"#94DDF4\",label=\"normal_snv_bam_readcount_tsv\"];\n    \"germline_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"germline_filtered_vcf\"];\n    \"small_candidates\" [fillcolor=\"#94DDF4\",label=\"small_candidates\"];\n    \"chart\" [fillcolor=\"#94DDF4\",label=\"chart\"];\n    \"combined_filtered_epitopes\" [fillcolor=\"#94DDF4\",label=\"combined_filtered_epitopes\"];\n    \"summary_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"summary_hs_metrics\"];\n    \"optitype_plot\" [fillcolor=\"#94DDF4\",label=\"optitype_plot\"];\n    \"verify_bam_id_depth\" [fillcolor=\"#94DDF4\",label=\"verify_bam_id_depth\"];\n    \"transcript_abundance_h5\" [fillcolor=\"#94DDF4\",label=\"transcript_abundance_h5\"];\n    \"gene_abundance\" [fillcolor=\"#94DDF4\",label=\"gene_abundance\"];\n    \"final_bam\" [fillcolor=\"#94DDF4\",label=\"final_bam\"];\n    \"normal_verify_bam_id_depth\" [fillcolor=\"#94DDF4\",label=\"normal_verify_bam_id_depth\"];\n    \"insert_size_metrics\" [fillcolor=\"#94DDF4\",label=\"insert_size_metrics\"];\n    \"pindel_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"pindel_filtered_vcf\"];\n    \"tumor_only_variants\" [fillcolor=\"#94DDF4\",label=\"tumor_only_variants\"];\n    \"combined_all_epitopes\" [fillcolor=\"#94DDF4\",label=\"combined_all_epitopes\"];\n    \"diploid_variants\" [fillcolor=\"#94DDF4\",label=\"diploid_variants\"];\n    \"strelka_unfiltered_vcf\" [fillcolor=\"#94DDF4\",label=\"strelka_unfiltered_vcf\"];\n    \"normal_cram\" [fillcolor=\"#94DDF4\",label=\"normal_cram\"];\n    \"phased_vcf\" [fillcolor=\"#94DDF4\",label=\"phased_vcf\"];\n    \"normal_target_coverage\" [fillcolor=\"#94DDF4\",label=\"normal_target_coverage\"];\n    \"mhc_i_all_epitopes\" [fillcolor=\"#94DDF4\",label=\"mhc_i_all_epitopes\"];\n    \"hs_metrics\" [fillcolor=\"#94DDF4\",label=\"hs_metrics\"];\n    \"somalier_concordance_metrics\" [fillcolor=\"#94DDF4\",label=\"somalier_concordance_metrics\"];\n    \"varscan_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"varscan_filtered_vcf\"];\n    \"gvcf\" [fillcolor=\"#94DDF4\",label=\"gvcf\"];\n    \"tumor_per_target_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_per_target_hs_metrics\"];\n    \"cn_diagram\" [fillcolor=\"#94DDF4\",label=\"cn_diagram\"];\n    \"all_candidates\" [fillcolor=\"#94DDF4\",label=\"all_candidates\"];\n    \"tumor_per_base_coverage_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_per_base_coverage_metrics\"];\n    \"tumor_mark_duplicates_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_mark_duplicates_metrics\"];\n    \"tumor_segmented_ratios\" [fillcolor=\"#94DDF4\",label=\"tumor_segmented_ratios\"];\n    \"tumor_verify_bam_id_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_verify_bam_id_metrics\"];\n    \"mhc_ii_ranked_epitopes\" [fillcolor=\"#94DDF4\",label=\"mhc_ii_ranked_epitopes\"];\n    \"cn_scatter_plot\" [fillcolor=\"#94DDF4\",label=\"cn_scatter_plot\"];\n    \"pindel_unfiltered_vcf\" [fillcolor=\"#94DDF4\",label=\"pindel_unfiltered_vcf\"];\n    \"normal_verify_bam_id_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_verify_bam_id_metrics\"];\n    \"varscan_unfiltered_vcf\" [fillcolor=\"#94DDF4\",label=\"varscan_unfiltered_vcf\"];\n    \"reference_coverage\" [fillcolor=\"#94DDF4\",label=\"reference_coverage\"];\n    \"flagstats\" [fillcolor=\"#94DDF4\",label=\"flagstats\"];\n    \"tumor_insert_size_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_insert_size_metrics\"];\n    \"tumor_snv_bam_readcount_tsv\" [fillcolor=\"#94DDF4\",label=\"tumor_snv_bam_readcount_tsv\"];\n    \"tumor_summary_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_summary_hs_metrics\"];\n    \"normal_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_hs_metrics\"];\n    \"somatic_final_vcf\" [fillcolor=\"#94DDF4\",label=\"somatic_final_vcf\"];\n    \"mhc_i_ranked_epitopes\" [fillcolor=\"#94DDF4\",label=\"mhc_i_ranked_epitopes\"];\n    \"tumor_verify_bam_id_depth\" [fillcolor=\"#94DDF4\",label=\"tumor_verify_bam_id_depth\"];\n    \"stringtie_transcript_gtf\" [fillcolor=\"#94DDF4\",label=\"stringtie_transcript_gtf\"];\n    \"tumor_bin_level_ratios\" [fillcolor=\"#94DDF4\",label=\"tumor_bin_level_ratios\"];\n    \"normal_per_base_coverage_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_per_base_coverage_metrics\"];\n    \"mhc_ii_all_epitopes\" [fillcolor=\"#94DDF4\",label=\"mhc_ii_all_epitopes\"];\n    \"combined_ranked_epitopes\" [fillcolor=\"#94DDF4\",label=\"combined_ranked_epitopes\"];\n    \"alignment_summary_metrics\" [fillcolor=\"#94DDF4\",label=\"alignment_summary_metrics\"];\n    \"tumor_alignment_summary_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_alignment_summary_metrics\"];\n    \"tumor_antitarget_coverage\" [fillcolor=\"#94DDF4\",label=\"tumor_antitarget_coverage\"];\n    \"normal_per_target_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_per_target_hs_metrics\"];\n    \"stringtie_gene_expression_tsv\" [fillcolor=\"#94DDF4\",label=\"stringtie_gene_expression_tsv\"];\n    \"normal_mark_duplicates_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_mark_duplicates_metrics\"];\n    \"normal_per_base_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_per_base_hs_metrics\"];\n    \"final_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"final_filtered_vcf\"];\n    \"metrics\" [fillcolor=\"#94DDF4\",label=\"metrics\"];\n    \"insert_size_histogram\" [fillcolor=\"#94DDF4\",label=\"insert_size_histogram\"];\n    \"normal_alignment_summary_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_alignment_summary_metrics\"];\n    \"tumor_per_target_coverage_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_per_target_coverage_metrics\"];\n    \"normal_antitarget_coverage\" [fillcolor=\"#94DDF4\",label=\"normal_antitarget_coverage\"];\n    \"tumor_target_coverage\" [fillcolor=\"#94DDF4\",label=\"tumor_target_coverage\"];\n    \"mhc_i_filtered_epitopes\" [fillcolor=\"#94DDF4\",label=\"mhc_i_filtered_epitopes\"];\n    \"germline_final_vcf\" [fillcolor=\"#94DDF4\",label=\"germline_final_vcf\"];\n    \"annotated_tsv\" [fillcolor=\"#94DDF4\",label=\"annotated_tsv\"];\n    \"somalier_concordance_statistics\" [fillcolor=\"#94DDF4\",label=\"somalier_concordance_statistics\"];\n    \"final_tsv\" [fillcolor=\"#94DDF4\",label=\"final_tsv\"];\n    \"normal_summary_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_summary_hs_metrics\"];\n    \"hla_call_files\" [fillcolor=\"#94DDF4\",label=\"hla_call_files\"];\n    \"mhc_ii_filtered_epitopes\" [fillcolor=\"#94DDF4\",label=\"mhc_ii_filtered_epitopes\"];\n    \"per_target_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"per_target_hs_metrics\"];\n    \"tumor_per_base_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_per_base_hs_metrics\"];\n    \"mark_duplicates_metrics\" [fillcolor=\"#94DDF4\",label=\"mark_duplicates_metrics\"];\n    \"intervals_target\" [fillcolor=\"#94DDF4\",label=\"intervals_target\"];\n    \"mutect_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"mutect_filtered_vcf\"];\n    \"tumor_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_hs_metrics\"];\n    \"normal_per_target_coverage_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_per_target_coverage_metrics\"];\n    \"per_base_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"per_base_hs_metrics\"];\n    \"per_base_coverage_metrics\" [fillcolor=\"#94DDF4\",label=\"per_base_coverage_metrics\"];\n    \"optitype_tsv\" [fillcolor=\"#94DDF4\",label=\"optitype_tsv\"];\n    \"verify_bam_id_metrics\" [fillcolor=\"#94DDF4\",label=\"verify_bam_id_metrics\"];\n    \"normal_insert_size_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_insert_size_metrics\"];\n    \"germline_vep_summary\" [fillcolor=\"#94DDF4\",label=\"germline_vep_summary\"];\n    \"somatic_variants\" [fillcolor=\"#94DDF4\",label=\"somatic_variants\"];\n    \"docm_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"docm_filtered_vcf\"];\n    \"per_target_coverage_metrics\" [fillcolor=\"#94DDF4\",label=\"per_target_coverage_metrics\"];\n    \"consensus_alleles\" [fillcolor=\"#94DDF4\",label=\"consensus_alleles\"];\n    \"allele_string\" [fillcolor=\"#94DDF4\",label=\"allele_string\"];\n    \"normal_flagstats\" [fillcolor=\"#94DDF4\",label=\"normal_flagstats\"];\n    \"normal_indel_bam_readcount_tsv\" [fillcolor=\"#94DDF4\",label=\"normal_indel_bam_readcount_tsv\"];\n    \"mutect_unfiltered_vcf\" [fillcolor=\"#94DDF4\",label=\"mutect_unfiltered_vcf\"];\n  }\n  \"extract_alleles\" [label=\"extract_alleles\"];\n  \"hla_consensus\" [label=\"Script to create consensus from optitype and clinical HLA typing\"];\n  \"phase_vcf\" [label=\"phase VCF\", fillcolor=\"#F3CEA1\"];\n  \"pvacseq\" [label=\"Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs\", fillcolor=\"#F3CEA1\"];\n  \"rnaseq\" [label=\"RNA-Seq alignment and transcript/gene abundance workflow\", fillcolor=\"#F3CEA1\"];\n  \"somatic\" [label=\"somatic_exome: exome alignment and somatic variant detection\", fillcolor=\"#F3CEA1\"];\n  \"germline\" [label=\"exome alignment and germline variant detection, with optitype for HLA typing\", fillcolor=\"#F3CEA1\"];\n  \"germline\" -> \"extract_alleles\" [label=\"allele_file\"];\n  \"extract_alleles\" -> \"hla_consensus\" [label=\"optitype_hla_alleles\"];\n  \"clinical_hla_alleles\" -> \"hla_consensus\" [label=\"clinical_hla_alleles\"];\n  \"somatic\" -> \"phase_vcf\" [label=\"bam\"];\n  \"reference\" -> \"phase_vcf\" [label=\"reference\"];\n  \"reference_dict\" -> \"phase_vcf\" [label=\"reference_dict\"];\n  \"tumor_sample_name\" -> \"phase_vcf\" [label=\"tumor_sample_name\"];\n  \"normal_sample_name\" -> \"phase_vcf\" [label=\"normal_sample_name\"];\n  \"somatic\" -> \"phase_vcf\" [label=\"somatic_vcf\"];\n  \"germline\" -> \"phase_vcf\" [label=\"germline_vcf\"];\n  \"tumor_sample_name\" -> \"pvacseq\" [label=\"sample_name\"];\n  \"rnaseq\" -> \"pvacseq\" [label=\"transcript_expression_file\"];\n  \"normal_sample_name\" -> \"pvacseq\" [label=\"normal_sample_name\"];\n  \"hla_consensus\" -> \"pvacseq\" [label=\"alleles\"];\n  \"binding_threshold\" -> \"pvacseq\" [label=\"binding_threshold\"];\n  \"expn_val\" -> \"pvacseq\" [label=\"expn_val\"];\n  \"prediction_algorithms\" -> \"pvacseq\" [label=\"prediction_algorithms\"];\n  \"maximum_transcript_support_level\" -> \"pvacseq\" [label=\"maximum_transcript_support_level\"];\n  \"reference\" -> \"pvacseq\" [label=\"reference_fasta\"];\n  \"tdna_vaf\" -> \"pvacseq\" [label=\"tdna_vaf\"];\n  \"fasta_size\" -> \"pvacseq\" [label=\"fasta_size\"];\n  \"trna_cov\" -> \"pvacseq\" [label=\"trna_cov\"];\n  \"top_score_metric\" -> \"pvacseq\" [label=\"top_score_metric\"];\n  \"rnaseq\" -> \"pvacseq\" [label=\"gene_expression_file\"];\n  \"readcount_minimum_mapping_quality\" -> \"pvacseq\" [label=\"readcount_minimum_mapping_quality\"];\n  \"additional_report_columns\" -> \"pvacseq\" [label=\"additional_report_columns\"];\n  \"normal_cov\" -> \"pvacseq\" [label=\"normal_cov\"];\n  \"exclude_nas\" -> \"pvacseq\" [label=\"exclude_nas\"];\n  \"phase_vcf\" -> \"pvacseq\" [label=\"phased_proximal_variants_vcf\"];\n  \"tdna_cov\" -> \"pvacseq\" [label=\"tdna_cov\"];\n  \"pvacseq_threads\" -> \"pvacseq\" [label=\"n_threads\"];\n  \"somatic\" -> \"pvacseq\" [label=\"detect_variants_vcf\"];\n  \"vep_to_table_fields\" -> \"pvacseq\" [label=\"vep_to_table_fields\"];\n  \"readcount_minimum_base_quality\" -> \"pvacseq\" [label=\"readcount_minimum_base_quality\"];\n  \"netmhc_stab\" -> \"pvacseq\" [label=\"netmhc_stab\"];\n  \"variants_to_table_fields\" -> \"pvacseq\" [label=\"variants_to_table_fields\"];\n  \"rnaseq\" -> \"pvacseq\" [label=\"rnaseq_bam\"];\n  \"allele_specific_binding_thresholds\" -> \"pvacseq\" [label=\"allele_specific_binding_thresholds\"];\n  \"peptide_sequence_length\" -> \"pvacseq\" [label=\"peptide_sequence_length\"];\n  \"net_chop_threshold\" -> \"pvacseq\" [label=\"net_chop_threshold\"];\n  \"trna_vaf\" -> \"pvacseq\" [label=\"trna_vaf\"];\n  \"epitope_lengths\" -> \"pvacseq\" [label=\"epitope_lengths\"];\n  \"minimum_fold_change\" -> \"pvacseq\" [label=\"minimum_fold_change\"];\n  \"net_chop_method\" -> \"pvacseq\" [label=\"net_chop_method\"];\n  \"downstream_sequence_length\" -> \"pvacseq\" [label=\"downstream_sequence_length\"];\n  \"variants_to_table_genotype_fields\" -> \"pvacseq\" [label=\"variants_to_table_genotype_fields\"];\n  \"normal_vaf\" -> \"pvacseq\" [label=\"normal_vaf\"];\n  \"refFlat\" -> \"rnaseq\" [label=\"refFlat\"];\n  \"rna_readgroups\" -> \"rnaseq\" [label=\"read_group_id\"];\n  \"trimming_adapter_min_overlap\" -> \"rnaseq\" [label=\"trimming_adapter_min_overlap\"];\n  \"trimming_min_readlength\" -> \"rnaseq\" [label=\"trimming_min_readlength\"];\n  \"trimming_max_uncalled\" -> \"rnaseq\" [label=\"trimming_max_uncalled\"];\n  \"sample_name\" -> \"rnaseq\" [label=\"sample_name\"];\n  \"rna_bams\" -> \"rnaseq\" [label=\"instrument_data_bams\"];\n  \"read_group_fields\" -> \"rnaseq\" [label=\"read_group_fields\"];\n  \"vep_ensembl_species\" -> \"rnaseq\" [label=\"species\"];\n  \"strand\" -> \"rnaseq\" [label=\"strand\"];\n  \"ribosomal_intervals\" -> \"rnaseq\" [label=\"ribosomal_intervals\"];\n  \"kallisto_index\" -> \"rnaseq\" [label=\"kallisto_index\"];\n  \"vep_ensembl_assembly\" -> \"rnaseq\" [label=\"assembly\"];\n  \"reference_annotation\" -> \"rnaseq\" [label=\"reference_annotation\"];\n  \"gene_transcript_lookup_table\" -> \"rnaseq\" [label=\"gene_transcript_lookup_table\"];\n  \"trimming_adapters\" -> \"rnaseq\" [label=\"trimming_adapters\"];\n  \"trimming_adapter_trim_end\" -> \"rnaseq\" [label=\"trimming_adapter_trim_end\"];\n  \"reference_index\" -> \"rnaseq\" [label=\"reference_index\"];\n  \"docm_vcf\" -> \"somatic\" [label=\"docm_vcf\"];\n  \"synonyms_file\" -> \"somatic\" [label=\"synonyms_file\"];\n  \"mutect_max_alt_allele_in_normal_fraction\" -> \"somatic\" [label=\"mutect_max_alt_allele_in_normal_fraction\"];\n  \"interval_list\" -> \"somatic\" [label=\"interval_list\"];\n  \"vep_ensembl_assembly\" -> \"somatic\" [label=\"vep_ensembl_assembly\"];\n  \"filter_docm_variants\" -> \"somatic\" [label=\"filter_docm_variants\"];\n  \"pindel_insert_size\" -> \"somatic\" [label=\"pindel_insert_size\"];\n  \"tumor_sequence\" -> \"somatic\" [label=\"tumor_sequence\"];\n  \"summary_intervals\" -> \"somatic\" [label=\"summary_intervals\"];\n  \"per_base_intervals\" -> \"somatic\" [label=\"per_base_intervals\"];\n  \"tumor_name\" -> \"somatic\" [label=\"tumor_name\"];\n  \"mutect_artifact_detection_mode\" -> \"somatic\" [label=\"mutect_artifact_detection_mode\"];\n  \"vep_to_table_fields\" -> \"somatic\" [label=\"vep_to_table_fields\"];\n  \"varscan_min_var_freq\" -> \"somatic\" [label=\"varscan_min_var_freq\"];\n  \"vep_pick\" -> \"somatic\" [label=\"vep_pick\"];\n  \"dbsnp_vcf\" -> \"somatic\" [label=\"dbsnp_vcf\"];\n  \"vep_custom_annotations\" -> \"somatic\" [label=\"vep_custom_annotations\"];\n  \"reference\" -> \"somatic\" [label=\"reference\"];\n  \"annotate_coding_only\" -> \"somatic\" [label=\"annotate_coding_only\"];\n  \"somalier_vcf\" -> \"somatic\" [label=\"somalier_vcf\"];\n  \"picard_metric_accumulation_level\" -> \"somatic\" [label=\"picard_metric_accumulation_level\"];\n  \"varscan_min_coverage\" -> \"somatic\" [label=\"varscan_min_coverage\"];\n  \"known_indels\" -> \"somatic\" [label=\"known_indels\"];\n  \"qc_minimum_mapping_quality\" -> \"somatic\" [label=\"qc_minimum_mapping_quality\"];\n  \"varscan_strand_filter\" -> \"somatic\" [label=\"varscan_strand_filter\"];\n  \"normal_name\" -> \"somatic\" [label=\"normal_name\"];\n  \"mutect_scatter_count\" -> \"somatic\" [label=\"mutect_scatter_count\"];\n  \"vep_ensembl_version\" -> \"somatic\" [label=\"vep_ensembl_version\"];\n  \"omni_vcf\" -> \"somatic\" [label=\"omni_vcf\"];\n  \"normal_sample_name\" -> \"somatic\" [label=\"normal_sample_name\"];\n  \"target_intervals\" -> \"somatic\" [label=\"target_intervals\"];\n  \"qc_minimum_base_quality\" -> \"somatic\" [label=\"qc_minimum_base_quality\"];\n  \"varscan_max_normal_freq\" -> \"somatic\" [label=\"varscan_max_normal_freq\"];\n  \"variants_to_table_fields\" -> \"somatic\" [label=\"variants_to_table_fields\"];\n  \"variants_to_table_genotype_fields\" -> \"somatic\" [label=\"variants_to_table_genotype_fields\"];\n  \"cle_vcf_filter\" -> \"somatic\" [label=\"cle_vcf_filter\"];\n  \"tumor_sample_name\" -> \"somatic\" [label=\"tumor_sample_name\"];\n  \"mutect_max_alt_alleles_in_normal_count\" -> \"somatic\" [label=\"mutect_max_alt_alleles_in_normal_count\"];\n  \"manta_call_regions\" -> \"somatic\" [label=\"manta_call_regions\"];\n  \"manta_non_wgs\" -> \"somatic\" [label=\"manta_non_wgs\"];\n  \"manta_output_contigs\" -> \"somatic\" [label=\"manta_output_contigs\"];\n  \"vep_ensembl_species\" -> \"somatic\" [label=\"vep_ensembl_species\"];\n  \"known_variants\" -> \"somatic\" [label=\"known_variants\"];\n  \"panel_of_normals_vcf\" -> \"somatic\" [label=\"panel_of_normals_vcf\"];\n  \"mills\" -> \"somatic\" [label=\"mills\"];\n  \"bqsr_intervals\" -> \"somatic\" [label=\"bqsr_intervals\"];\n  \"varscan_p_value\" -> \"somatic\" [label=\"varscan_p_value\"];\n  \"normal_sequence\" -> \"somatic\" [label=\"normal_sequence\"];\n  \"vep_cache_dir\" -> \"somatic\" [label=\"vep_cache_dir\"];\n  \"cosmic_vcf\" -> \"somatic\" [label=\"cosmic_vcf\"];\n  \"strelka_cpu_reserved\" -> \"somatic\" [label=\"strelka_cpu_reserved\"];\n  \"bait_intervals\" -> \"somatic\" [label=\"bait_intervals\"];\n  \"per_target_intervals\" -> \"somatic\" [label=\"per_target_intervals\"];\n  \"per_target_intervals\" -> \"germline\" [label=\"per_target_intervals\"];\n  \"vep_custom_annotations\" -> \"germline\" [label=\"vep_custom_annotations\"];\n  \"summary_intervals\" -> \"germline\" [label=\"summary_intervals\"];\n  \"vep_ensembl_assembly\" -> \"germline\" [label=\"vep_ensembl_assembly\"];\n  \"bait_intervals\" -> \"germline\" [label=\"bait_intervals\"];\n  \"gatk_haplotypecaller_intervals\" -> \"germline\" [label=\"intervals\"];\n  \"gvcf_gq_bands\" -> \"germline\" [label=\"gvcf_gq_bands\"];\n  \"picard_metric_accumulation_level\" -> \"germline\" [label=\"picard_metric_accumulation_level\"];\n  \"per_base_intervals\" -> \"germline\" [label=\"per_base_intervals\"];\n  \"known_indels\" -> \"germline\" [label=\"known_indels\"];\n  \"target_intervals\" -> \"germline\" [label=\"target_intervals\"];\n  \"annotate_coding_only\" -> \"germline\" [label=\"annotate_coding_only\"];\n  \"dbsnp_vcf\" -> \"germline\" [label=\"dbsnp_vcf\"];\n  \"reference\" -> \"germline\" [label=\"reference\"];\n  \"vep_cache_dir\" -> \"germline\" [label=\"vep_cache_dir\"];\n  \"omni_vcf\" -> \"germline\" [label=\"omni_vcf\"];\n  \"synonyms_file\" -> \"germline\" [label=\"synonyms_file\"];\n  \"mills\" -> \"germline\" [label=\"mills\"];\n  \"emit_reference_confidence\" -> \"germline\" [label=\"emit_reference_confidence\"];\n  \"vep_ensembl_version\" -> \"germline\" [label=\"vep_ensembl_version\"];\n  \"normal_sequence\" -> \"germline\" [label=\"sequence\"];\n  \"qc_minimum_base_quality\" -> \"germline\" [label=\"qc_minimum_base_quality\"];\n  \"qc_minimum_mapping_quality\" -> \"germline\" [label=\"qc_minimum_mapping_quality\"];\n  \"optitype_name\" -> \"germline\" [label=\"optitype_name\"];\n  \"vep_ensembl_species\" -> \"germline\" [label=\"vep_ensembl_species\"];\n  \"bqsr_intervals\" -> \"germline\" [label=\"bqsr_intervals\"];\n  \"germline\" -> \"cram\";\n  \"pvacseq\" -> \"annotated_vcf\";\n  \"somatic\" -> \"intervals_antitarget\";\n  \"somatic\" -> \"somatic_vep_summary\";\n  \"rnaseq\" -> \"transcript_abundance_tsv\";\n  \"somatic\" -> \"tumor_cram\";\n  \"somatic\" -> \"strelka_filtered_vcf\";\n  \"somatic\" -> \"tumor_flagstats\";\n  \"somatic\" -> \"tumor_indel_bam_readcount_tsv\";\n  \"somatic\" -> \"normal_snv_bam_readcount_tsv\";\n  \"germline\" -> \"germline_filtered_vcf\";\n  \"somatic\" -> \"small_candidates\";\n  \"rnaseq\" -> \"chart\";\n  \"pvacseq\" -> \"combined_filtered_epitopes\";\n  \"germline\" -> \"summary_hs_metrics\";\n  \"germline\" -> \"optitype_plot\";\n  \"germline\" -> \"verify_bam_id_depth\";\n  \"rnaseq\" -> \"transcript_abundance_h5\";\n  \"rnaseq\" -> \"gene_abundance\";\n  \"rnaseq\" -> \"final_bam\";\n  \"somatic\" -> \"normal_verify_bam_id_depth\";\n  \"germline\" -> \"insert_size_metrics\";\n  \"somatic\" -> \"pindel_filtered_vcf\";\n  \"somatic\" -> \"tumor_only_variants\";\n  \"pvacseq\" -> \"combined_all_epitopes\";\n  \"somatic\" -> \"diploid_variants\";\n  \"somatic\" -> \"strelka_unfiltered_vcf\";\n  \"somatic\" -> \"normal_cram\";\n  \"phase_vcf\" -> \"phased_vcf\";\n  \"somatic\" -> \"normal_target_coverage\";\n  \"pvacseq\" -> \"mhc_i_all_epitopes\";\n  \"germline\" -> \"hs_metrics\";\n  \"somatic\" -> \"somalier_concordance_metrics\";\n  \"somatic\" -> \"varscan_filtered_vcf\";\n  \"germline\" -> \"gvcf\";\n  \"somatic\" -> \"tumor_per_target_hs_metrics\";\n  \"somatic\" -> \"cn_diagram\";\n  \"somatic\" -> \"all_candidates\";\n  \"somatic\" -> \"tumor_per_base_coverage_metrics\";\n  \"somatic\" -> \"tumor_mark_duplicates_metrics\";\n  \"somatic\" -> \"tumor_segmented_ratios\";\n  \"somatic\" -> \"tumor_verify_bam_id_metrics\";\n  \"pvacseq\" -> \"mhc_ii_ranked_epitopes\";\n  \"somatic\" -> \"cn_scatter_plot\";\n  \"somatic\" -> \"pindel_unfiltered_vcf\";\n  \"somatic\" -> \"normal_verify_bam_id_metrics\";\n  \"somatic\" -> \"varscan_unfiltered_vcf\";\n  \"somatic\" -> \"reference_coverage\";\n  \"germline\" -> \"flagstats\";\n  \"somatic\" -> \"tumor_insert_size_metrics\";\n  \"somatic\" -> \"tumor_snv_bam_readcount_tsv\";\n  \"somatic\" -> \"tumor_summary_hs_metrics\";\n  \"somatic\" -> \"normal_hs_metrics\";\n  \"somatic\" -> \"somatic_final_vcf\";\n  \"pvacseq\" -> \"mhc_i_ranked_epitopes\";\n  \"somatic\" -> \"tumor_verify_bam_id_depth\";\n  \"rnaseq\" -> \"stringtie_transcript_gtf\";\n  \"somatic\" -> \"tumor_bin_level_ratios\";\n  \"somatic\" -> \"normal_per_base_coverage_metrics\";\n  \"pvacseq\" -> \"mhc_ii_all_epitopes\";\n  \"pvacseq\" -> \"combined_ranked_epitopes\";\n  \"germline\" -> \"alignment_summary_metrics\";\n  \"somatic\" -> \"tumor_alignment_summary_metrics\";\n  \"somatic\" -> \"tumor_antitarget_coverage\";\n  \"somatic\" -> \"normal_per_target_hs_metrics\";\n  \"rnaseq\" -> \"stringtie_gene_expression_tsv\";\n  \"somatic\" -> \"normal_mark_duplicates_metrics\";\n  \"somatic\" -> \"normal_per_base_hs_metrics\";\n  \"somatic\" -> \"final_filtered_vcf\";\n  \"rnaseq\" -> \"metrics\";\n  \"germline\" -> \"insert_size_histogram\";\n  \"somatic\" -> \"normal_alignment_summary_metrics\";\n  \"somatic\" -> \"tumor_per_target_coverage_metrics\";\n  \"somatic\" -> \"normal_antitarget_coverage\";\n  \"somatic\" -> \"tumor_target_coverage\";\n  \"pvacseq\" -> \"mhc_i_filtered_epitopes\";\n  \"germline\" -> \"germline_final_vcf\";\n  \"pvacseq\" -> \"annotated_tsv\";\n  \"somatic\" -> \"somalier_concordance_statistics\";\n  \"somatic\" -> \"final_tsv\";\n  \"somatic\" -> \"normal_summary_hs_metrics\";\n  \"hla_consensus\" -> \"hla_call_files\";\n  \"pvacseq\" -> \"mhc_ii_filtered_epitopes\";\n  \"germline\" -> \"per_target_hs_metrics\";\n  \"somatic\" -> \"tumor_per_base_hs_metrics\";\n  \"germline\" -> \"mark_duplicates_metrics\";\n  \"somatic\" -> \"intervals_target\";\n  \"somatic\" -> \"mutect_filtered_vcf\";\n  \"somatic\" -> \"tumor_hs_metrics\";\n  \"somatic\" -> \"normal_per_target_coverage_metrics\";\n  \"germline\" -> \"per_base_hs_metrics\";\n  \"germline\" -> \"per_base_coverage_metrics\";\n  \"germline\" -> \"optitype_tsv\";\n  \"germline\" -> \"verify_bam_id_metrics\";\n  \"somatic\" -> \"normal_insert_size_metrics\";\n  \"germline\" -> \"germline_vep_summary\";\n  \"somatic\" -> \"somatic_variants\";\n  \"somatic\" -> \"docm_filtered_vcf\";\n  \"germline\" -> \"per_target_coverage_metrics\";\n  \"hla_consensus\" -> \"consensus_alleles\";\n  \"extract_alleles\" -> \"allele_string\";\n  \"somatic\" -> \"normal_flagstats\";\n  \"somatic\" -> \"normal_indel_bam_readcount_tsv\";\n  \"somatic\" -> \"mutect_unfiltered_vcf\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/038cb3617a1966a1057386adcde97ce55d9e1139/definitions/pipelines/immuno.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/genome/analysis-workflows/blob/038cb3617a1966a1057386adcde97ce55d9e1139/definitions/pipelines/immuno.cwl","visualisationPng":"/graph/png/github.com/genome/analysis-workflows/blob/038cb3617a1966a1057386adcde97ce55d9e1139/definitions/pipelines/immuno.cwl","visualisationSvg":"/graph/svg/github.com/genome/analysis-workflows/blob/038cb3617a1966a1057386adcde97ce55d9e1139/definitions/pipelines/immuno.cwl","roBundle":"/robundle/github.com/genome/analysis-workflows/blob/038cb3617a1966a1057386adcde97ce55d9e1139/definitions/pipelines/immuno.cwl","licenseName":"MIT License"}