pipeline/wdl/statistics.wdl

# statistics

task run_statistics {
    String name
    String output_dir
    String rmdupBam

    String ref
    String bed

    command {

        if [ ! -d ${output_dir}/qc/${name}_bamdst ];then
        mkdir -p ${output_dir}/qc/${name}_bamdst
        fi

        samtools flagstat -@ 10 ${rmdupBam} >${output_dir}/qc/${name}.rmdup.flagstat
        samtools stats --reference ${ref} -t ${bed} -@ 10 ${rmdupBam} > ${output_dir}/qc/${name}.rmdup.stat
        bamdst -p ${bed} -o ${output_dir}/qc/${name}_bamdst ${rmdupBam}
        qc_stat.py ${output_dir}/qc/${name}.json ${output_dir}/qc/${name}_bamdst/ ${output_dir}/qc/${name}_qc.txt

        #        InsertAndDepthStat.R \
        #        ${output_dir}/qc/${name}_InsertAndDepthStat \
        #        ${output_dir}/qc/${name}_bamdst/insertsize.plot \
        #        ${output_dir}/qc/${name}_bamdst/depth_distribution.plot
    }
}

task run_statistics_umi {
    String name
    String output_dir
    String sortedBam
    String rmdupBam
    String genecore_json

    String ref
    String bed

    command {

        if [ ! -d ${output_dir}/qc/${name}_bamdst ];then
        mkdir -p ${output_dir}/qc/${name}_bamdst
        mkdir -p ${output_dir}/qc/${name}_sorted_bamdst
        fi

        samtools flagstat -@ 10 ${rmdupBam} >${output_dir}/qc/${name}.rmdup.flagstat
        samtools stats --reference ${ref} -t ${bed} -@ 10 ${rmdupBam} > ${output_dir}/qc/${name}.rmdup.stat
        bamdst -p ${bed} -o ${output_dir}/qc/${name}_bamdst ${rmdupBam}
        bamdst -p ${bed} -o ${output_dir}/qc/${name}_sorted_bamdst ${sortedBam}

        qc_stat_umi.py ${output_dir}/qc/${name}.json ${output_dir}/qc/${name}_bamdst/ ${output_dir}/qc/${name}_sorted_bamdst/ ${genecore_json} ${output_dir}/qc/${name}_qc.txt

        #        InsertAndDepthStat.R \
        #        ${output_dir}/qc/${name}_InsertAndDepthStat \
        #        ${output_dir}/qc/${name}_bamdst/insertsize.plot \
        #        ${output_dir}/qc/${name}_bamdst/depth_distribution.plot
    }
}

workflow statistics {
    Boolean run=true

    Boolean umi

    String tumor
    String tumor_rmdup_bam
    String tumor_sorted_bam

    String? normal
    String? normal_rmdup_bam

    String genecore_json

    String ref
    String bed
    String output_dir

    if (run) {
        if (umi) {
            call run_statistics_umi as runstatistics_umi_tumor {
                input:
                    name=tumor,
                    output_dir=output_dir,
                    rmdupBam=tumor_rmdup_bam,
                    genecore_json=genecore_json,
                    sortedBam=tumor_sorted_bam,
                    ref=ref,
                    bed=bed
            }
        }

        if (!umi) {
            call run_statistics as runstatistics_tumor {
                input:
                    name=tumor,
                    output_dir=output_dir,
                    rmdupBam=tumor_rmdup_bam,
                    ref=ref,
                    bed=bed
            }
        }

        if (defined(normal)) {
            call run_statistics as runstatistics_normal {
                input:
                    name=normal,
                    output_dir=output_dir,
                    rmdupBam=normal_rmdup_bam,
                    ref=ref,
                    bed=bed
            }
        }
    }

    output {
        String tumor_bamdst_depth = "${output_dir}/qc/${tumor}_bamdst/depth.tsv.gz"
    }
}