......

defaults

@@ -9,7 +9,7 @@
     "stringtie_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/stringtie:v1.3.4", 
     "stringtie_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc", 
     "fastp_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastp:0.19.6", 
-    "fastp_cluster": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc", 
+    "fastp_cluster": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc", 
     "fasta": "GRCh38.d1.vd1.fa", 
     "fastqc_disk_size": "150", 
     "gtf": "oss://pgx-reference-data/reference/annotation/Homo_sapiens.GRCh38.93.gtf", 

tasks/fastp.wdl

@@ -44,15 +44,7 @@ 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_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 ${max_len2} /
-        -i /cromwell_root/tmp/fastp/${sample_id}_R1.fastq.tmp2.gz -I /cromwell_root/tmp/fastp/${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 ${max_len2} -i /cromwell_root/tmp/fastp/${sample_id}_R1.fastq.tmp2.gz -I /cromwell_root/tmp/fastp/${sample_id}_R2.fastq.tmp2.gz -o ${sample_id}_R1.fastq.gz -O ${sample_id}_R2.fastq.gz -j ${sample_id}.json -h ${sample_id}.html
         else
 	cp /cromwell_root/tmp/fastp/${sample_id}_R1.fastq.tmp2.gz ${sample_id}_R1.fastq.gz
 	cp /cromwell_root/tmp/fastp/${sample_id}_R2.fastq.tmp2.gz ${sample_id}_R2.fastq.gz
@@ -72,7 +64,4 @@ task fastp {
       File Trim_R1 = "${sample_id}_R1.fastq.gz"
       File Trim_R2 = "${sample_id}_R2.fastq.gz"
    }
-}
-
-
-
+}