#/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 - $import: ../types/vep_custom_annotation.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? #somatic inputs reference: type: - string - File secondaryFiles: [.fai, ^.dict, .amb, .ann, .bwt, .pac, .sa] label: "reference: Reference fasta file for a desired assembly" doc: | reference contains the nucleotide sequence for a given assembly (hg37, hg38, etc.) in fasta format for the entire genome. This is what reads will be aligned to. Appropriate files can be found on ensembl at https://ensembl.org/info/data/ftp/index.html When providing the reference secondary files corresponding to reference indices must be located in the same directory as the reference itself. These files can be created with samtools index, bwa index, and picard CreateSequenceDictionary. tumor_sequence: type: ../types/sequence_data.yml#sequence_data[] 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 sequencing data for single sample (i.e. fastq files). If more than one fastq file exist for a sample, as in the case for multiple instrument data, the sequence tag is simply repeated with the additional data (see example input file). Note that in the @RG field ID and SM are required. tumor_name: type: string? default: 'tumor' 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 outputs, for exmaple the VCF files. normal_sequence: type: ../types/sequence_data.yml#sequence_data[] 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 sequencing data for single sample (i.e. fastq files). If more than one fastq file exist for a sample, as in the case for multiple instrument data, the sequence tag is simply repeated with the additional data (see example input file). Note that in the @RG field ID and SM are required. normal_name: type: string? default: 'normal' 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 outputs, for exmaple the VCF files. bqsr_known_sites: type: File[] secondaryFiles: [.tbi] label: "bqsr_known_sites: One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis." doc: | Known polymorphic indels recommended by GATK for a variety of tools including the BaseRecalibrator. This is part of the GATK resource bundle available at http://www.broadinstitute.org/gatk/guide/article?id=1213 File should be in vcf format, and tabix indexed. bqsr_intervals: type: string[] 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 GATK base quality score recalibrations. Typically intervals are given for the entire chromosome (i.e. chr1, chr2, etc.), these names should match the format in the reference file. bait_intervals: type: File 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. These are essentially coordinates for regions you were able to design probes for in the reagent. Typically the reagent provider has this information available in bed format and it can be converted to an interval_list with Picard BedToIntervalList. AstraZeneca also maintains a repo of baits for common sequencing reagents available at https://github.com/AstraZeneca-NGS/reference_data target_intervals: type: File 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 capture reagent. BED files with this information can be converted to interval_lists with Picard BedToIntervalList. In general for a WES exome reagent bait_intervals and target_intervals are the same. target_interval_padding: type: int label: "target_interval_padding: number of bp flanking each target region in which to allow variant calls" doc: | The effective coverage of capture products generally extends out beyond the actual regions targeted. This parameter allows variants to be called in these wingspan regions, extending this many base pairs from each side of the target regions. default: 100 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 strelka_cpu_reserved: type: int? default: 8 scatter_count: type: int doc: "scatters each supported variant detector (varscan, pindel, mutect) into this many parallel jobs" 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] doc: "Common mutations in cancer that will be genotyped and passed through into the merged VCF if they have even low-level evidence of a mutation (by default, marked with filter DOCM_ONLY)" filter_docm_variants: type: boolean? default: true doc: "Determines whether variants found only via genotyping of DOCM sites will be filtered (as DOCM_ONLY) or passed through as variant calls" vep_cache_dir: type: - string - Directory 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] vep_custom_annotations: type: ../types/vep_custom_annotation.yml#vep_custom_annotation[] doc: "custom type, check types directory for input format" manta_call_regions: type: File? secondaryFiles: [.tbi] manta_non_wgs: type: boolean? default: true manta_output_contigs: type: boolean? somalier_vcf: type: File known_variants: type: File? secondaryFiles: [.tbi] doc: "Previously discovered variants to be flagged in this pipelines's output vcf" #germline inputs emit_reference_confidence: type: type: enum symbols: ['NONE', 'BP_RESOLUTION', 'GVCF'] gvcf_gq_bands: type: string[] gatk_haplotypecaller_intervals: type: type: array items: type: array items: string ploidy: type: int? optitype_name: type: string? #phase_vcf inputs reference_dict: type: File clinical_mhc_classI_alleles: type: string[]? label: "Clinical HLA typing results, limited to MHC Class I alleles; element format: HLA-X*01:02[/HLA-X...]" doc: "used to provide clinical HLA typing results in the format HLA-X*01:02[/HLA-X...] when available." clinical_mhc_classII_alleles: type: string[]? label: "Clinical HLA typing results, limited to MHC Class II alleles" doc: "used to provide clinical HLA typing results; separated from class I due to nomenclature inconsistencies" #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"] 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). C-term 3.0 is trained with publicly available MHC class I ligands and the authors believe that is performs best in predicting the boundaries of CTL epitopes. 20S is trained with in vitro degradation data. net_chop_threshold: type: float? label: "net_chop_threshold: NetChop prediction threshold" doc: | net_chop_threshold specifies the threshold to use for NetChop prediction; increasing the threshold results in better specificity, but worse sensitivity. netmhc_stab: type: boolean? 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. pvacseq_threads: type: int? 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. tumor_sample_name: type: string label: "tumor_sample_name: Name of the tumor sample" doc: | tumor_sample_name is the name of the tumor sample being processed. When processing a multi-sample VCF the sample name must be a sample ID in the input VCF #CHROM header line. normal_sample_name: type: string label: "tumor_sample_name: Name of the normal sample" doc: | normal_sample_name is the name of the normal sample to use for phasing of germline variants. outputs: final_bam: type: File outputSource: rnaseq/final_bam secondaryFiles: [.bai] label: "Sorted BAM from tumor RNA" doc: | Sorted BAM file of sequencing read alignments by HISAT2 with duplicate reads tagged stringtie_transcript_gtf: type: File outputSource: rnaseq/stringtie_transcript_gtf label: "Transcript GTF assembled from tumor RNA by StringTie" doc: | GTF file containing the transcripts assembled from the tumor RNA sample, created by StringTie stringtie_gene_expression_tsv: type: File outputSource: rnaseq/stringtie_gene_expression_tsv label: "Gene abundance table from tumor RNA by StringTie" doc: | Tab-delimited file containing gene abundances in FPKM and TPM, created by StringTie transcript_abundance_tsv: type: File outputSource: rnaseq/transcript_abundance_tsv label: "Transcript-level abundance table by kallisto" doc: | Tab-delimited file containing transcript-level abundance estimates in TPM, created by kallisto transcript_abundance_h5: type: File outputSource: rnaseq/transcript_abundance_h5 label: "Transcript-level abundance table in HDF5 format by kallisto" doc: | HDF5 binary file containing transcript-level abundance esimates, bootstrap estimate, and so on, created by kallisto gene_abundance: type: File outputSource: rnaseq/gene_abundance label: "Gene-level abundance output by tximport with kallisto output" doc: | Tab-delimited file containing the abundance estimates summarized in the gene level with kallisto output by Bioconductor tximport tool metrics: type: File outputSource: rnaseq/metrics label: "RNA-seq Diagnosis/quality metrics from tumor RNA" doc: | RNA-seq Diagnosis/quality metrics showing the distribution of the bases within the transcripts, created by picard CollectRnaSeqMetrics tool chart: type: File? outputSource: rnaseq/chart label: "Plot for RNA-seq diagnosis/quality metrics" doc: | PDF file for the plot of RNA sequencing coverage at the normalized position across transcript as RNA-seq diagnosis/quality metrics, created by picard CollectRnaSeqMetrics tool tumor_cram: type: File outputSource: somatic/tumor_cram label: "Sorted CRAM from tumor DNA" doc: | Sorted CRAM file of sequencing read alignments by bwa-mem from a tumor DNA sample with duplicate reads tagged tumor_mark_duplicates_metrics: type: File outputSource: somatic/tumor_mark_duplicates_metrics label: "Sequencing duplicate metrics from tumor DNA" doc: | Duplication metrics on duplicate sequencing reads from a tumor DNA sample, identified by picard MarkDuplicates tool tumor_insert_size_metrics: type: File outputSource: somatic/tumor_insert_size_metrics label: "Paired-end sequencing diagnosis/quality metrics from tumor DNA" doc: | Diagnosis/quality metrics including the insert size distribution and read orientation of the paired-end libraries from a tumor DNA sample tumor_alignment_summary_metrics: type: File outputSource: somatic/tumor_alignment_summary_metrics label: "Sequencign alignment summary from tumor DNA" doc: | Diagnosis/quality metrics summarizing the quality of sequencing read alignments from a tumor DNA sample, reported by the picard CollectAlignmentSummaryMetrics tool tumor_hs_metrics: type: File outputSource: somatic/tumor_hs_metrics label: "Sequencing coverage summary of target intervals from tumor DNA" doc: | Diagnosis/quality metrics specific for sequencing data generated through hybrid-selection (e.g. whole exome) from a tumor DNA sample, for example to assess target coverage of WES tumor_per_target_coverage_metrics: type: File[] outputSource: somatic/tumor_per_target_coverage_metrics label: "Sequencing per-target coverage summary of target intervals from tumor DNA" doc: | Diagnosis/quality metrics showing detailed sequencing coverage per target interval (optional, 59 genes recommended by ACMG for clinical exome and genome sequencing for example) from a tumor DNA sample tumor_per_target_hs_metrics: type: File[] outputSource: somatic/tumor_per_target_hs_metrics label: "Sequencing coverage summary of target intervals from tumor DNA" doc: | Diagnosis/quality metrics for sequencing coverage for target intervals (optional, 59 genes recommended by ACMG for clinical exome and genome sequencing for example) from a tumor DNA sample tumor_per_base_coverage_metrics: type: File[] outputSource: somatic/tumor_per_base_coverage_metrics label: "Sequencing per-base coverage summary at target sites from tumor DNA" doc: | Diagnosis/quality metrics showing detailed sequencing coverage per target site (optional, known variant sites of clinical significance from ClinVar for example) from a tumor DNA sample tumor_per_base_hs_metrics: type: File[] outputSource: somatic/tumor_per_base_hs_metrics label: "Sequencing coverage summary at target sites from tumor DNA" doc: | Diagnosis/quality metrics for sequencing coverage at target sites (optional, known variant sites of clinical significance from ClinVar for example) from a tumor DNA sample tumor_summary_hs_metrics: type: File[] outputSource: somatic/tumor_summary_hs_metrics tumor_flagstats: type: File outputSource: somatic/tumor_flagstats label: "Sequencing count metrics based on SAM FLAG field from tumor sample" doc: | Summary with the count numbers of alignments for each FLAG type from a tumor DNA sample, including 13 categories based on the bit flags in the FLAG field tumor_verify_bam_id_metrics: type: File outputSource: somatic/tumor_verify_bam_id_metrics label: "Sequencing quality assessment metric for tumor sample contamination" doc: | verifyBamID output files containing the contamination estimate in a tumor DNA sample, across all readGroups and per readGroup separately tumor_verify_bam_id_depth: type: File outputSource: somatic/tumor_verify_bam_id_depth label: "Sequencing quality assessment metric for tumor sample genotyping" doc: | verifyBamID output files showing the sequencing depth distribution at the marker positions from Omni genotype data with a tumor DNA sample, across all readGroups and per readGroup separately normal_cram: type: File outputSource: somatic/normal_cram label: "Sorted CRAM from normal DNA" doc: | Sorted CRAM file of sequencing read alignments by bwa-mem from a normal DNA sample with duplicate reads tagged normal_mark_duplicates_metrics: type: File outputSource: somatic/normal_mark_duplicates_metrics label: "Sequencing duplicate metrics from normal DNA" doc: | Duplication metrics on duplicate sequencing reads from a normal DNA sample, identified by picard MarkDuplicates tool normal_insert_size_metrics: type: File outputSource: somatic/normal_insert_size_metrics label: "Paired-end sequencing diagnosis/quality metrics from normal DNA" doc: | Diagnosis/quality metrics including the insert size distribution and read orientation of the paired-end libraries from a normal DNA sample normal_alignment_summary_metrics: type: File outputSource: somatic/normal_alignment_summary_metrics label: "Sequencign alignment summary from normal DNA" doc: | Diagnosis/quality metrics summarizing the quality of sequencing read alignments from a normal DNA sample, reported by the picard CollectAlignmentSummaryMetrics tool normal_hs_metrics: type: File outputSource: somatic/normal_hs_metrics label: "Sequencing coverage summary of target intervals from normal DNA" doc: | Diagnosis/quality metrics specific for sequencing data generated through hybrid-selection (e.g. whole exome) from a normal DNA sample, for example to assess target coverage normal_per_target_coverage_metrics: type: File[] outputSource: somatic/normal_per_target_coverage_metrics label: "Sequencing per-target coverage summary of target intervals from normal DNA" doc: | Diagnosis/quality metrics showing detailed sequencing coverage per target interval (optional, 59 genes recommended by ACMG for clinical exome and genome sequencing for example) from a normal DNA sample normal_per_target_hs_metrics: type: File[] outputSource: somatic/normal_per_target_hs_metrics label: "Sequencing coverage summary of target intervals from normal DNA" doc: | Diagnosis/quality metrics for sequencing coverage for target intervals (optional, 59 genes recommended by ACMG for clinical exome and genome sequencing for example) from a normal DNA sample normal_per_base_coverage_metrics: type: File[] outputSource: somatic/normal_per_base_coverage_metrics label: "Sequencing per-base coverage summary at target sites from normal DNA" doc: | Diagnosis/quality metrics showing detailed sequencing coverage per target site (optional, known variant sites of clinical significance from ClinVar for example) from a normal DNA sample normal_per_base_hs_metrics: type: File[] outputSource: somatic/normal_per_base_hs_metrics label: "Sequencing coverage summary at target sites from normal DNA" doc: | Diagnosis/quality metrics for sequencing coverage at target sites (optional, known variant sites of clinical significance from ClinVar for example) from a normal DNA sample normal_summary_hs_metrics: type: File[] outputSource: somatic/normal_summary_hs_metrics normal_flagstats: type: File outputSource: somatic/normal_flagstats label: "Sequencing count metrics based on SAM FLAG field from normal sample" doc: | Summary with the count numbers of alignments for each FLAG type from a normal DNA sample, including 13 categories based on the bit flags in the FLAG field normal_verify_bam_id_metrics: type: File outputSource: somatic/normal_verify_bam_id_metrics label: "Sequencing quality assessment metric for normal sample contamination" doc: | verifyBamID output files containing the contamination estimate in a normal DNA sample, across all readGroups and per readGroup separately normal_verify_bam_id_depth: type: File outputSource: somatic/normal_verify_bam_id_depth label: "Sequencing quality assessment metric for normal sample genotyping" doc: | verifyBamID output files showing the sequencing depth distribution at the marker positions from Omni genotype data with a normal DNA sample, across all readGroups and per readGroup separately 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 germline_raw_vcf: type: File outputSource: germline/raw_vcf secondaryFiles: [.tbi] germline_final_vcf: type: File outputSource: germline/final_vcf secondaryFiles: [.tbi] germline_filtered_vcf: type: File outputSource: germline/filtered_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 consensus_alleles: type: string[] outputSource: hla_consensus/consensus_alleles hla_call_files: type: Directory outputSource: hla_consensus/hla_call_files annotated_vcf: type: File outputSource: pvacseq/annotated_vcf annotated_tsv: type: File outputSource: pvacseq/annotated_tsv pvacseq_predictions: type: Directory outputSource: pvacseq/pvacseq_predictions 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 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] somatic: run: somatic_exome.cwl in: reference: reference tumor_sequence: tumor_sequence tumor_name: tumor_name normal_sequence: normal_sequence normal_name: normal_name bqsr_known_sites: bqsr_known_sites bqsr_intervals: bqsr_intervals bait_intervals: bait_intervals target_intervals: target_intervals target_interval_padding: target_interval_padding 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 strelka_cpu_reserved: strelka_cpu_reserved scatter_count: 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 vep_custom_annotations: vep_custom_annotations manta_call_regions: manta_call_regions manta_non_wgs: manta_non_wgs manta_output_contigs: manta_output_contigs somalier_vcf: somalier_vcf tumor_sample_name: tumor_sample_name normal_sample_name: normal_sample_name known_variants: known_variants 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 bqsr_known_sites: bqsr_known_sites 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 ploidy: ploidy vep_cache_dir: vep_cache_dir vep_ensembl_assembly: vep_ensembl_assembly vep_ensembl_version: vep_ensembl_version vep_ensembl_species: vep_ensembl_species vep_custom_annotations: vep_custom_annotations synonyms_file: synonyms_file annotate_coding_only: annotate_coding_only qc_minimum_mapping_quality: qc_minimum_mapping_quality qc_minimum_base_quality: qc_minimum_base_quality 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,raw_vcf,final_vcf,filtered_vcf,vep_summary,optitype_tsv,optitype_plot] phase_vcf: run: ../subworkflows/phase_vcf.cwl in: somatic_vcf: somatic/final_filtered_vcf germline_vcf: germline/final_vcf reference: reference reference_dict: reference_dict bam: somatic/tumor_cram normal_sample_name: normal_sample_name tumor_sample_name: tumor_sample_name out: [phased_vcf] extract_alleles: run: ../tools/extract_hla_alleles.cwl in: allele_file: germline/optitype_tsv out: [allele_string] hla_consensus: run: ../tools/hla_consensus.cwl in: optitype_hla_alleles: extract_alleles/allele_string clinical_mhc_classI_alleles: clinical_mhc_classI_alleles clinical_mhc_classII_alleles: clinical_mhc_classII_alleles out: [consensus_alleles, hla_call_files] pvacseq: run: ../subworkflows/pvacseq.cwl in: detect_variants_vcf: somatic/final_filtered_vcf sample_name: tumor_sample_name normal_sample_name: 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: hla_consensus/consensus_alleles 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, pvacseq_predictions]