lncRNAseq/tasks/featureCounts.wdl

task featureCounts {
    File bam_file
    File lnc_gtf_file = "lncRNAKB_hg38_v7.gtf"
    String gtf_dir = "oss://pgx-reference-data/reference/subread/"
    String sample_id
    String docker
    String cluster
    Int cpu_num = 4
    Int strand_information = 0

    
    command <<<
        mkdir -p $sample_id
        featureCounts -T $cpu_num -t exon -g gene_id -a $gtf_dir/$lnc_gtf_file -s $strand_information -p -o $sample_id/$sample_id.genefeaturecount.txt $bam_file
    >>>

    runtime {
        docker: docker
        cluster: cluster
        systemDisk: "cloud_ssd 40"
        dataDisk: "cloud_ssd 200 /cromwell_root/"
    }

    output {
        File out_profile = "${sample_id}.genefeaturecount.txt"
        File out_summary = "${sample_id}.summary"
    }
}