task pathseq {
    String sample_id
    File fastq1
    File fastq2
    File host_image
    File host_kmer
    File microbe_dict
    File microbe_bwa_image
    File microbe_taxonomy

    String disk_size
    String docker
    String cluster

    command <<<
	
        set -o pipefail
        set -e

        mkdir ubam
        mkdir filter_log
        mkdir clean_pair_bam
        mkdir clean_unpaired_bam
        mkdir pathseq_result
        mkdir bwa_pair_bam
        mkdir bwa_pair_unpair_bam

        gatk FastqToSam \
            -F1 ${fastq1} \
            -F2 ${fastq2} \
            -O ./ubam/${sample_id}.bam \
            -SM ${sample_id}

        time gatk --java-options "-Xmx58g" PathSeqFilterSpark  \
            --input ./ubam/${sample_id}.bam \
            --paired-output ./clean_pair_bam/${sample_id}_paired.bam \
            --unpaired-output ./clean_unpaired_bam/${sample_id}_unpaired.bam \
            --min-clipped-read-length 70 \
            --kmer-file ${host_kmer} \
            --filter-bwa-image ${host_image} \
            --filter-metrics filter_log/${sample_id}.log 

        time gatk --java-options "-Xmx58g" PathSeqBwaSpark  \
            --paired-input ./clean_pair_bam/${sample_id}_paired.bam \
            --unpaired-input ./clean_unpaired_bam/${sample_id}_unpaired.bam \
            --paired-output bwa_pair_bam/${sample_id}_bwa_paired.bam \
            --unpaired-output bwa_unpair_bam/${sample_id}_bwa_unpaired.bam \
            --microbe-bwa-image ${microbe_bwa_image} \
            --microbe-dict ${microbe_dict}


        time gatk --java-options "-Xmx58g" PathSeqScoreSpark  \
            --paired-input bwa_pair_bam/${sample_id}_bwa_paired.bam \
            --unpaired-input bwa_unpair_bam/${sample_id}_bwa_unpaired.bam \
            --taxonomy-file ${microbe_taxonomy} \
            --scores-output pathseq_result/${sample_id}.pathseq.txt \
            --output pathseq_result/${sample_id}.pathseq_reads.bam \
            --min-score-identity 0.90 \
            --identity-margin 0.02

        

    >>>
	
    runtime {
        docker: docker
        cluster: cluster
        systemDisk: "cloud_ssd 40"
        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
    }

    output {
        File pathseq_txt = "pathseq_result/${sample_id}.pathseq.txt"
        File pathseq_bam = "pathseq_result/${sample_id}.pathseq_reads.bam"
        File pathseq_sbi = "pathseq_result/${sample_id}.pathseq_reads.bam.sbi"
    }

}