......

defaults

@@ -37,10 +37,10 @@
     "adapter_sequence_r2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT", 
     "disable_adapter_trimming": "0", 
     "length_required": "50", 
+    "length_required1": "20", 
     "UMI": "0", 
     "umi_len": "0", 
     "umi_loc": "umi_loc", 
-    "length_required": "20", 
     "qualified_quality_phred": "20", 
     "disable_quality_filtering": "0"
 }

inputs

@@ -37,11 +37,11 @@
 	"{{ project_name }}.adapter_sequence": "{{ adapter_sequence }}",
 	"{{ project_name }}.adapter_sequence_r2": "{{ adapter_sequence_r2 }}",
 	"{{ project_name }}.disable_adapter_trimming": "{{ disable_adapter_trimming }}",
-	"{{ project_name }}.length_required": "{{ length_required }}",
 	"{{ project_name }}.UMI": "{{ UMI }}",
 	"{{ project_name }}.umi_loc": "{{ umi_loc }}",
 	"{{ project_name }}.umi_len": "{{ umi_len }}",
 	"{{ project_name }}.length_required": "{{ length_required }}",
+	"{{ project_name }}.length_required1": "{{ length_required1 }}",
 	"{{ project_name }}.qualified_quality_phred": "{{ qualified_quality_phred }}",
 	"{{ project_name }}.disable_quality_filtering": "{{ disable_quality_filtering }}"
 }

tasks/fastp.wdl

@@ -41,7 +41,7 @@ task fastp {
 	##3.Trim
         if [ ${disable_adapter_trimming} -gt 0 ]
         then
-	fastp --thread 4 -l ${length_required} -q ${qualified_quality_phred} -u ${length_required}  --adapter_sequence ${adapter_sequence} --adapter_sequence_r2 ${adapter_sequence_r2} --detect_adapter_for_pe --trim_front1 ${trim_front1} --trim_tail1 ${trim_tail1} --max_len1 ${max_len1} --trim_front2 ${trim_front2} --trim_tail2 ${trim_tail2} --max_len2 ${max_len2} -i ${sample_id}_R1.fastq.tmp2.gz -I ${sample_id}_R2.fastq.tmp2.gz -o ${sample_id}_R1.fastq.gz -O ${sample_id}_R2.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} --adapter_sequence_r2 ${adapter_sequence_r2} --detect_adapter_for_pe --trim_front1 ${trim_front1} --trim_tail1 ${trim_tail1} --max_len1 ${max_len1} --trim_front2 ${trim_front2} --trim_tail2 ${trim_tail2} --max_len2 ${max_len2} -i ${sample_id}_R1.fastq.tmp2.gz -I ${sample_id}_R2.fastq.tmp2.gz -o ${sample_id}_R1.fastq.gz -O ${sample_id}_R2.fastq.gz -j ${sample_id}.json -h ${sample_id}.html
         else
 	mv ${sample_id}_R1.fastq.tmp2.gz ${sample_id}_R1.fastq.gz
 	mv ${sample_id}_R2.fastq.tmp2.gz ${sample_id}_R2.fastq.gz