immuno.cwl

#/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: MT sequencing data and readgroup information"
        doc: |
          tumor_sequence represents the sequencing data for the MT sample as either FASTQs or BAMs with
          accompanying readgroup information. 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 example the VCF files.
    normal_sequence:
        type: ../types/sequence_data.yml#sequence_data[]
        label: "normal_sequence: WT sequencing data and readgroup information"
        doc: |
          normal_sequence represents the sequencing data for the WT sample as either FASTQs or BAMs with
          accompanying readgroup information. 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 example 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 (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
    validated_variants:
        type: File?
        secondaryFiles: [.tbi]
        doc: "An optional VCF with variants that will be flagged as 'VALIDATED' if found in this pipeline's main 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_bigwig:
        type: File
        outputSource: rnaseq/bamcoverage_bigwig
    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: reference
            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, bamcoverage_bigwig]
    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
            validated_variants: validated_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]
    intersect_passing_variants:
        run: ../tools/intersect_known_variants.cwl
        in:
            vcf: somatic/final_filtered_vcf
            validated_variants: validated_variants
        out:
            [validated_and_pipeline_vcf]
    pvacseq:
        run: ../subworkflows/pvacseq.cwl
        in:
            detect_variants_vcf: intersect_passing_variants/validated_and_pipeline_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]