first commit

tasks/fastp.wdl

@@ -38,7 +38,7 @@ task fastp {
 	##3.Trim
         if [ "${disable_adapter_trimming}" == 0 ]
         then
-	fastp --thread 4 -l ${length_required} -q ${qualified_quality_phred} -u ${length_required1} --adapter_sequence ${adapter_sequence} --adapter_sequence --trim_front1 ${trim_front1} --trim_tail1 ${trim_tail1} -i /cromwell_root/tmp/fastp/${sample_id}.fastq.tmp2.gz -o ${sample_id}.fastq.gz -j ${sample_id}.json -h ${sample_id}.html
+	fastp --thread 4 -l ${length_required} -q ${qualified_quality_phred} -u ${length_required1} --adapter_sequence ${adapter_sequence} --trim_front1 ${trim_front1} --trim_tail1 ${trim_tail1} -i /cromwell_root/tmp/fastp/${sample_id}.fastq.tmp2.gz -o ${sample_id}.fastq.gz -j ${sample_id}.json -h ${sample_id}.html
         else
 	cp /cromwell_root/tmp/fastp/${sample_id}.fastq.tmp2.gz ${sample_id}.fastq.gz
         fi