remove fastp useless paramater

defaults

@@ -10,20 +10,8 @@
     "fastqc_cluster": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
     "fastp_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastp:0.19.6",
     "fastp_cluster": "OnDemand bcs.a2.xlarge img-ubuntu-vpc",
-    "trim_front1": "0",
-    "trim_tail1": "0",
-    "max_len1": "0",
-    "trim_front2": "0",
-    "trim_tail2": "0",
-    "max_len2": "0",
     "adapter_sequence": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCA",
     "adapter_sequence_r2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT",
-    "disable_adapter_trimming": "0",
-    "length_required": "50",
-    "length_required1": "20",
-    "umi_len": "0",
-    "umi_loc": "umi_loc",
-    "qualified_quality_phred": "20",
     "hisat2_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/hisat2:v2.1.0-2",
     "hisat2_cluster": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
     "samtools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/samtools:v1.3.1",

inputs

@@ -14,22 +14,8 @@
     "{{ project_name }}.fastqc_docker": "{{ fastqc_docker }}",
     "{{ project_name }}.fastp_docker": "{{ fastp_docker }}",
     "{{ project_name }}.fastp_cluster": "{{ fastp_cluster }}",
-    "{{ project_name }}.trim_front1": "{{ trim_front1 }}",
-    "{{ project_name }}.trim_tail1": "{{ trim_tail1 }}",
-    "{{ project_name }}.max_len1": "{{ max_len1 }}",
-    "{{ project_name }}.trim_front2": "{{ trim_front2 }}",
-    "{{ 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 }}",
-    "{{ project_name }}.umi_loc": "{{ umi_loc }}",
-    "{{ project_name }}.umi_len": "{{ umi_len }}",
-    "{{ project_name }}.length_required": "{{ length_required }}",
-    "{{ project_name }}.qualified_quality_phred": "{{ qualified_quality_phred }}",
-    "{{ project_name }}.disable_quality_filtering": "{{ disable_quality_filtering }}",
     "{{ project_name }}.hisat2_docker": "{{ hisat2_docker }}",
     "{{ project_name }}.hisat2_cluster": "{{ hisat2_cluster }}",
     "{{ project_name }}.insert_size": "{{ insert_size }}",

tasks/fastp.wdl

@@ -7,18 +7,7 @@ task fastp {
     String docker
     String cluster
     String disk_size
-    String umi_loc	
     String trim_adapter
-    Int trim_front1
-    Int trim_tail1
-    Int max_len1
-    Int trim_front2
-    Int trim_tail2
-    Int max_len2
-    Int length_required
-    Int umi_len
-    Int qualified_quality_phred
-    Int length_required1
 
 	command <<<
     nt=$(nproc)
@@ -28,7 +17,7 @@ task fastp {
     cp ${read1} ${sample_id}_R1.fq.gz
     cp ${read2} ${sample_id}_R2.fq.gz
     else
-    fastp --thread $nt -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 ${read1} -I ${read2} -o ${sample_id}_R1.fq.gz -O ${sample_id}_R2.fq.gz -j ${sample_id}.json -h ${sample_id}.html
+    fastp --thread $nt --adapter_sequence ${adapter_sequence} --adapter_sequence_r2 ${adapter_sequence_r2} --detect_adapter_for_pe -i ${read1} -I ${read2} -o ${sample_id}_R1.fq.gz -O ${sample_id}_R2.fq.gz -j ${sample_id}.json -h ${sample_id}.html
     fi
    >>>
    

workflow.wdl

@@ -26,7 +26,6 @@ workflow {{ project_name }} {
 	String fastp_cluster
 	String adapter_sequence
 	String adapter_sequence_r2
-	String umi_loc
 	String hisat2_docker
 	String hisat2_cluster
 	String idx_prefix
@@ -43,16 +42,6 @@ workflow {{ project_name }} {
 	String count_length
 	String sample_id
 
-	Int trim_front1
-	Int trim_tail1
-	Int max_len1
-	Int trim_front2
-	Int trim_tail2
-	Int max_len2
-	Int length_required
-	Int umi_len
-	Int qualified_quality_phred
-	Int length_required1
 	Int insert_size
 
 	Boolean pre_alignment_qc
@@ -91,17 +80,6 @@ workflow {{ project_name }} {
 		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,
-		max_len1=max_len1,
-		trim_front2=trim_front2,
-		trim_tail2=trim_tail2,
-		max_len2=max_len2,
-		length_required=length_required,
-		umi_len=umi_len,
-		qualified_quality_phred=qualified_quality_phred,
-		length_required1=length_required1,
 		trim_adapter=trim_adapter
 		}