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 docker_fastp
    String docker_bowtie

    String cluster_config
    String disk_size

    String adapter_seq
    Int randomBase_in_adapter
    
    Int qualified_quality_phred
    Int unqualified_percent_limit
    Int n_base_limit
    Int length_required

    File dir_index_mature
    String prefix_index_mature
    Int sum_unmatch_quality_limit

    call TrimAdapt.TrimAdapt as TrimAdapt {
        input:
            sample_ID=sample_ID,in_fastq=raw_fastq,
            adapter_seq=adapter_seq, randomBase_in_adapter=randomBase_in_adapter,
            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.Align as Align2Mature {
        input:
            sample_ID=sample_ID,
            in_fastq=ReadFilter.out_fastq,
            dir_index=dir_index_mature,prefix_index=prefix_index_mature,
            sum_unmatch_quality_limit=sum_unmatch_quality_limit,
            docker=docker_bowtie, cluster_config=cluster_config, disk_size=disk_size
    }

    call Quantification.Quantification as Quantification{
        input:
            sample_ID=sample_ID,
            in_sam=Align2Mature.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_mature=Align2Mature.out_log,
            cluster_config=cluster_config, disk_size=disk_size
    }

}