se_2156

defaults

@@ -8,7 +8,6 @@
     "trim_tail2": "0",
     "max_len2": "0",
     "adapter_sequence": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCA",
-    "adapter_sequence_r2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT",
     "disable_adapter_trimming": "0",
     "length_required": "50",
     "length_required1": "20",

inputs

@@ -10,7 +10,6 @@
 	"{{ project_name }}.trim_tail2": "{{ trim_tail2 }}",
 	"{{ project_name }}.max_len2": "{{ max_len2 }}",
 	"{{ 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_required1": "{{ length_required1 }}",
 	"{{ project_name }}.UMI": "{{ UMI }}",

tasks/fastp.wdl

@@ -2,7 +2,6 @@ task fastp {
     File read
     String sample_id=sub(basename(read), "\\.(fastq|fq)\\.gz$", "")
     String adapter_sequence
-    String adapter_sequence_r2
     String docker
     String cluster
     String disk_size

workflow.wdl

@@ -41,9 +41,6 @@ workflow {{ project_name }} {
 	Int trim_front1 
 	Int trim_tail1 
 	Int max_len1 
-	Int trim_front2 
-	Int trim_tail2  
-	Int max_len2 
 	Int disable_adapter_trimming
 	Int length_required
 	Int umi_len
@@ -80,7 +77,6 @@ workflow {{ project_name }} {
 		cluster = fastp_cluster,
 		disk_size = disk_size,
 		adapter_sequence = adapter_sequence,
-		adapter_sequence_r2 = adapter_sequence_r2,
 		umi_loc = umi_loc,
 		trim_front1 = trim_front1,
 		trim_tail1 = trim_tail1,