rnaseq_fastp/tasks/fastp.wdl

task fastp {
    String sample_id
    File read1
    File read2
    String adapter_sequence
    String adapter_sequence_r2
    String docker
    String cluster

   command <<<
     fastp --thread 4 -l 50 -q 20 -u 20 --adapter_sequence ${adapter_sequence} --adapter_sequence_r2 ${adapter_sequence_r2} --detect_adapter_for_pe -i  ${read1} -I ${read2} -o ${sample_id}_R1.fastq.gz -O ${sample_id}_R2.fastq.gz -j ${sample_id}.json -h ${sample_id}.html
   >>>
   
   runtime { 
		docker: docker 
		cluster: cluster
		systemDisk: "cloud_ssd 40"
		dataDisk: "cloud_ssd 200 /cromwell_root/"
   }

   output {
      File json = "${sample_id}.json"
      File report = "${sample_id}.html"
      File Trim_R1 = "${sample_id}_R1.fastq.gz"
      File Trim_R2 = "${sample_id}_R2.fastq.gz"
   }
}