更新 'tasks/fastp.wdl'

tasks/fastp.wdl

@@ -25,11 +25,14 @@ task fastp {
     String disk_size
 
 
-    String out1_name = sample_id+'clean_1.fastq'
-    String out2_name = sample_id+'clean_2.fastq'
+    String out1_name = sample_id+'clean_1.fastq.gz'
+    String out2_name = sample_id+'clean_2.fastq.gz'
 
     command <<<
-
+		set -o pipefail
+    	set -e
+    	nt=$(nproc)
+                  
         # basic command
         /opt/conda/bin/fastp \
         --in1 ${in1} \
@@ -39,13 +42,8 @@ task fastp {
         --json ${json} \
         --html ${html} \
         --report_title ${report_title} \
-        
-        # options 
-        ${ true="--phred64 " false="" phred64 } \
-        ${ "--reads_to_process " + reads_to_process } \
-        ${ true="--fix_mgi_id " false="" fix_mgi_id } \
-        ${ "--adapter_sequence " + adapter_sequence } \
-        ${ "--adapter_sequence_r2 " + adapter_sequence_r2 }
+        --thread $nt \
+        --length_required 30
 
     >>>