import "./tasks/Fastqc.wdl" as Fastqc
import "./tasks/TrimAdapt.wdl" as TrimAdapt
import "./tasks/ReadFilter.wdl" as ReadFilter
import "./tasks/Align.wdl" as Align
import "./tasks/Quantification.wdl" as Quantification
import "./tasks/ReadStats.wdl" as ReadStats

workflow {{ project_name }} {
    String sample_id
    File raw_fastq

    String adapter_seq
    Int randomBase_in_adapter
    Int sequencing_length

    Int qualified_quality_phred
    Int unqualified_percent_limit
    Int n_base_limit
    Int length_required

    Int max_mismatch_allowed

    File dir_index_miRNA
    String prefix_index_miRNA
    File dir_index_rn7
    String prefix_index_rn7

    String docker_fastqc
    String docker_fastp
    String docker_bowtie

    String cluster_config

    String disk_size

    call Fastqc.Fastqc as Fastqc {
        input:
            in_fastq=raw_fastq,
            docker=docker_fastqc, cluster_config=cluster_config, disk_size=disk_size
    }

    call TrimAdapt.TrimAdapt as TrimAdapt {
        input:
            sample_id=sample_id,in_fastq=raw_fastq,
            adapter_seq=adapter_seq, randomBase_in_adapter=randomBase_in_adapter, sequencing_length=sequencing_length,
            docker=docker_fastp, cluster_config=cluster_config, disk_size=disk_size
    }


    call ReadFilter.ReadFilter as ReadFilter {
        input:
            sample_id=sample_id,
            in_fastq=TrimAdapt.out_fastq,
            qualified_quality_phred=qualified_quality_phred,unqualified_percent_limit=unqualified_percent_limit,
            n_base_limit=n_base_limit,
            length_required=length_required,
            docker=docker_fastp, cluster_config=cluster_config, disk_size=disk_size
    }

    call Align.AlignToSenseOnly as Align2miRNA {
        input:
            sample_id=sample_id,
            in_fastq=ReadFilter.out_fastq,
            refname="miRNA",dir_index=dir_index_miRNA,prefix_index=prefix_index_miRNA,
            max_mismatch_allowed=max_mismatch_allowed,
            docker=docker_bowtie, cluster_config=cluster_config, disk_size=disk_size
    }

    call Align.AlignToBothStrand as Align2rn7 {
        input:
            sample_id=sample_id,
            in_fastq=ReadFilter.out_fastq,
            refname="rn7",dir_index=dir_index_rn7,prefix_index=prefix_index_rn7,
            max_mismatch_allowed=max_mismatch_allowed,
            docker=docker_bowtie, cluster_config=cluster_config, disk_size=disk_size
    }

    call Quantification.Quantification as Quantification {
        input:
            sample_id=sample_id,
            in_sam=Align2miRNA.out_sam,
            cluster_config=cluster_config,disk_size=disk_size
    }

    call ReadStats.ReadStats as ReadStats {
        input:
            sample_id=sample_id,
            in_log_trimAdatper=TrimAdapt.out_log,in_log_readFilter=ReadFilter.out_log,
            in_log_align_miRNA=Align2miRNA.out_log,in_log_align_rn7=Align2rn7.out_log,
            cluster_config=cluster_config,disk_size=disk_size
    }
}