#!/usr/bin/env cwl-runner

cwlVersion: v1.0
class: Workflow
label: "RNA-Seq alignment and transcript/gene abundance workflow"
requirements:
    - class: MultipleInputFeatureRequirement
    - class: SubworkflowFeatureRequirement
    - class: ScatterFeatureRequirement
    - class: InlineJavascriptRequirement
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
    instrument_data_bams:
        type: File[]
    read_group_id:
        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
    species:
        type: string
        doc: 'the species being analyzed, such as homo_sapiens or mus_musculus'
    assembly:
        type: string
        doc: 'the assembly used, such as GRCh37/38, GRCm37/38'
outputs:
    final_bam:
        type: File
        outputSource: mark_dup/sorted_bam
        secondaryFiles: [.bai]
    stringtie_transcript_gtf:
        type: File
        outputSource: stringtie/transcript_gtf
    stringtie_gene_expression_tsv:
        type: File
        outputSource: stringtie/gene_expression_tsv
    transcript_abundance_tsv:
        type: File
        outputSource: kallisto/expression_transcript_table
    transcript_abundance_h5:
        type: File
        outputSource: kallisto/expression_transcript_h5
    gene_abundance:
        type: File
        outputSource: transcript_to_gene/gene_abundance
    metrics:
        type: File
        outputSource: generate_qc_metrics/metrics
    chart:
        type: File
        outputSource: generate_qc_metrics/chart
    fusion_evidence:
        type: File
        outputSource: kallisto/fusion_evidence
steps:
    bam_to_trimmed_fastq_and_hisat_alignments:
        run: ../subworkflows/bam_to_trimmed_fastq_and_hisat_alignments.cwl
        scatter: [bam, read_group_id, read_group_fields]
        scatterMethod: dotproduct
        in:
            bam: instrument_data_bams
            read_group_id: read_group_id
            read_group_fields: read_group_fields
            adapters: trimming_adapters
            adapter_trim_end: trimming_adapter_trim_end
            adapter_min_overlap: trimming_adapter_min_overlap
            max_uncalled: trimming_max_uncalled
            min_readlength: trimming_min_readlength
            reference_index: reference_index
            strand: strand
        out:
            [fastqs,aligned_bam]
    kallisto:
        run: ../tools/kallisto.cwl
        in:
            kallisto_index: kallisto_index
            strand: strand
            fastqs: bam_to_trimmed_fastq_and_hisat_alignments/fastqs
        out:
            [expression_transcript_table,expression_transcript_h5,fusion_evidence]
    transcript_to_gene:
        run: ../tools/transcript_to_gene.cwl
        in:
            transcript_table_h5: kallisto/expression_transcript_h5
            gene_transcript_lookup_table: gene_transcript_lookup_table
        out:
            [gene_abundance]
    merge:
        run: ../tools/merge_bams.cwl
        in:
            bams: bam_to_trimmed_fastq_and_hisat_alignments/aligned_bam
        out:
            [merged_bam]
    index_bam:
        run: ../tools/index_bam.cwl
        in:
            bam: merge/merged_bam
        out:
            [indexed_bam]
    mark_dup:
        run: ../tools/mark_duplicates_and_sort.cwl
        in:
            bam: merge/merged_bam
            input_sort_order: 
                default: "coordinate"
        out:
            [sorted_bam, metrics_file]
    stringtie:
        run: ../tools/stringtie.cwl
        in:
            bam: mark_dup/sorted_bam
            reference_annotation: reference_annotation
            sample_name: sample_name
            strand: strand
        out:
            [transcript_gtf,gene_expression_tsv]
    generate_qc_metrics:
        run: ../tools/generate_qc_metrics.cwl
        in:
            refFlat: refFlat
            ribosomal_intervals: ribosomal_intervals
            strand: strand
            bam: index_bam/indexed_bam
        out:
            [metrics, chart]