#!/usr/bin/env cwl-runner

cwlVersion: v1.0
class: Workflow
label: "exome alignment and germline variant detection"
requirements:
    - class: SubworkflowFeatureRequirement
inputs:
    reference:
        type: string
    bam:
        type: File
    emit_reference_confidence:
        type: string
    gvcf_gq_bands:
        type: string[]
    intervals:
        type:
            type: array
            items:
                type: array
                items: string
    contamination_fraction:
        type: string?
    vep_cache_dir:
        type: string
    vep_ensembl_assembly:
        type: string
        doc: "genome assembly to use in vep. Examples: GRCh38 or GRCm38"
    vep_ensembl_version:
        type: string
        doc: "ensembl version - Must be present in the cache directory. Example: 95"
    vep_ensembl_species:
        type: string
        doc: "ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus"
    vep_plugins:
        type: string[]?
        default: [Downstream, Wildtype]
    synonyms_file:
        type: File?
    annotate_coding_only:
        type: boolean?
    custom_gnomad_vcf:
        type: File?
        secondaryFiles: [.tbi]
    limit_variant_intervals:
        type: File
    custom_clinvar_vcf:
        type: File?
        secondaryFiles: [.tbi]
    variants_to_table_fields:
        type: string[]?
        default: ['CHROM','POS','ID','REF','ALT']
    variants_to_table_genotype_fields:
        type: string[]?
    vep_to_table_fields:
        type: string[]?
    final_tsv_prefix:
        type: string?
        default: 'variants'
outputs:
    gvcf:
        type: File[]
        outputSource: haplotype_caller/gvcf
    final_vcf:
        type: File
        outputSource: index_annotated_vcf/indexed_vcf
        secondaryFiles: [.tbi]
    coding_vcf:
        type: File
        outputSource: index_coding_vcf/indexed_vcf
        secondaryFiles: [.tbi]
    limited_vcf:
        type: File
        outputSource: limit_variants/filtered_vcf
        secondaryFiles: [.tbi]
    vep_summary:
        type: File
        outputSource: annotate_variants/vep_summary
    final_tsv:
        type: File
        outputSource: add_vep_fields_to_table/annotated_variants_tsv
steps:
    haplotype_caller:
        run: gatk_haplotypecaller_iterator.cwl
        in:
            reference: reference
            bam: bam
            emit_reference_confidence: emit_reference_confidence
            gvcf_gq_bands: gvcf_gq_bands
            intervals: intervals
            contamination_fraction: contamination_fraction
        out:
            [gvcf]
    genotype_gvcfs:
        run: ../tools/gatk_genotypegvcfs.cwl
        in:
            reference: reference
            gvcfs: haplotype_caller/gvcf
        out:
            [genotype_vcf]
    annotate_variants:
        run: ../tools/vep.cwl
        in:
            vcf: genotype_gvcfs/genotype_vcf
            cache_dir: vep_cache_dir
            ensembl_assembly: vep_ensembl_assembly
            ensembl_version: vep_ensembl_version
            ensembl_species: vep_ensembl_species
            synonyms_file: synonyms_file
            coding_only: annotate_coding_only
            reference: reference
            custom_gnomad_vcf: custom_gnomad_vcf
            custom_clinvar_vcf: custom_clinvar_vcf
            plugins: vep_plugins
        out:
            [annotated_vcf, vep_summary]
    bgzip_annotated_vcf:
        run: ../tools/bgzip.cwl
        in:
            file: annotate_variants/annotated_vcf
        out:
            [bgzipped_file]
    index_annotated_vcf:
        run: ../tools/index_vcf.cwl
        in:
            vcf: bgzip_annotated_vcf/bgzipped_file
        out:
            [indexed_vcf]
    coding_variant_filter:
        run: ../tools/filter_vcf_coding_variant.cwl
        in:
            vcf: annotate_variants/annotated_vcf
        out:
            [filtered_vcf]
    bgzip_coding_vcf:
        run: ../tools/bgzip.cwl
        in:
            file: coding_variant_filter/filtered_vcf
        out:
            [bgzipped_file]
    index_coding_vcf:
        run: ../tools/index_vcf.cwl
        in:
            vcf: bgzip_coding_vcf/bgzipped_file
        out:
            [indexed_vcf]
    limit_variants:
        run: ../tools/select_variants.cwl
        in:
            reference: reference
            vcf: index_coding_vcf/indexed_vcf
            interval_list: limit_variant_intervals
            exclude_filtered:
                default: true
        out:
            [filtered_vcf]
    variants_to_table:
        run: ../tools/variants_to_table.cwl
        in:
            reference: reference
            vcf: limit_variants/filtered_vcf
            fields: variants_to_table_fields
            genotype_fields: variants_to_table_genotype_fields
        out:
            [variants_tsv]
    add_vep_fields_to_table:
        run: ../tools/add_vep_fields_to_table.cwl
        in:
            vcf: limit_variants/filtered_vcf
            vep_fields: vep_to_table_fields
            tsv: variants_to_table/variants_tsv
            prefix: final_tsv_prefix
        out: [annotated_variants_tsv]