class: Workflow
cwlVersion: v1.0
label: RD_Connect
inputs:
    -
        id: fastq_files
        type: 'File[]'
    -
        id: reference_genome
        type: 'File[]'
    -
        id: known_indels_file
        type: File
    -
        id: known_sites_file
        type: File
    -
        id: chromosome
        type: string
    -
        id: readgroup_str
        type: string
    -
        id: sample_name
        type: string
outputs:
    -
        id: metrics
        outputSource:
            - picard_markduplicates/output_metrics
        type: File
    -
        id: gvcf
        outputSource:
            - gatk_haplotype_caller/gvcf
        type: File
steps:
    -
        id: unzipped_known_sites
        in:
            - {id: known_sites_file, source: [known_sites_file]}
        out:
            - {id: unzipped_known_sites_file}
        run: gunzip_known_sites.cwl
    -
        id: gunzip
        in:
            - {id: reference_file, source: [reference_genome]}
        out:
            - {id: unzipped_fasta}
        run: gunzip.cwl
    -
        id: picard_dictionary
        in:
            - {id: reference_genome, source: [gunzip/unzipped_fasta]}
        out:
            - {id: dict}
        run: picard_dictionary.cwl
    -
        id: cutadapt2
        in:
            - {id: raw_sequences, source: [fastq_files]}
        out:
            - {id: trimmed_fastq}
        run: cutadapt-v.1.18.cwl
    -
        id: bwa_index
        in:
            - {id: reference_genome, source: [gunzip/unzipped_fasta]}
        out:
            - {id: output}
        run: bwa-index.cwl
    -
        id: samtools_index
        in:
            - {id: input, source: [gunzip/unzipped_fasta]}
        out:
            - {id: index_fai}
        run: samtools_index.cwl
    -
        id: bwa_mem
        in:
            - {id: sample_name, source: [sample_name]}
            - {id: trimmed_fastq, source: [cutadapt2/trimmed_fastq]}
            - {id: read_group, source: [readgroup_str]}
            - {id: reference_genome, source: [bwa_index/output]}
        out:
            - {id: aligned_sam}
        run: bwa-mem.cwl
    -
        id: samtools_sort
        in:
            - {id: input, source: [bwa_mem/aligned_sam]}
        out:
            - {id: sorted_bam}
        run: samtools_sort_bam.cwl
    -
        id: picard_markduplicates
        in:
            - {id: input, source: [samtools_sort/sorted_bam]}
        out:
            - {id: md_bam}
            - {id: output_metrics}
        run: picard_markduplicates.cwl
        label: picard-MD
    -
        id: gatk3-rtc
        in:
            - {id: input, source: [picard_markduplicates/md_bam]}
            - {id: reference_genome, source: [samtools_index/index_fai]}
            - {id: dict, source: [picard_dictionary/dict]}
            - {id: known_indels, source: [known_indels_file]}
        out:
            - {id: rtc_intervals_file}
        run: gatk3-rtc.cwl
        label: gatk3-rtc
    -
        id: gatk-ir
        in:
            - {id: input, source: [picard_markduplicates/md_bam]}
            - {id: rtc_intervals, source: [gatk3-rtc/rtc_intervals_file]}
            - {id: reference_genome, source: [samtools_index/index_fai]}
            - {id: dict, source: [picard_dictionary/dict]}
        out:
            - {id: realigned_bam}
        run: gatk-ir.cwl
        label: gatk-ir
    -
        id: gatk-base_recalibration
        in:
            - {id: reference_genome, source: [samtools_index/index_fai]}
            - {id: dict, source: [picard_dictionary/dict]}
            - {id: input, source: [gatk-ir/realigned_bam]}
            - {id: unzipped_known_sites_file, source: [unzipped_known_sites/unzipped_known_sites_file]}
            - {id: known_indels_file, source: [known_indels_file]}
        out:
            - {id: br_model}
        run: gatk-base_recalibration.cwl
        label: gatk-base_recalibration
    -
        id: gatk-base_recalibration_print_reads
        in:
            - {id: reference_genome, source: [samtools_index/index_fai]}
            - {id: dict, source: [picard_dictionary/dict]}
            - {id: input, source: [gatk-ir/realigned_bam]}
            - {id: br_model, source: [gatk-base_recalibration/br_model]}
        out:
            - {id: bqsr_bam}
        run: gatk-base_recalibration_print_reads.cwl
        label: gatk-base_recalibration_print_reads
    -
        id: gatk_haplotype_caller
        in:
            - {id: reference_genome, source: [samtools_index/index_fai]}
            - {id: dict, source: [picard_dictionary/dict]}
            - {id: input, source: [gatk-base_recalibration_print_reads/bqsr_bam]}
            - {id: chromosome, source: [chromosome]}
        out:
            - {id: gvcf}
        run: gatk-haplotype_caller.cwl
        label: gatk-haplotype_caller
requirements:
    -
        class: MultipleInputFeatureRequirement