更新 'tasks/fastq.wdl'

tasks/fastq.wdl

@@ -1,31 +1,5 @@
-version 1.0
 
-workflow fastp {
-    input{
-        Array[String] samples
-        File fastq_dir
-    }
-
-    scatter (sample_id in samples){
-        call pair_end{
-            input:
-            in1 = fastq_dir+'/'+sample_id+'_1.fastq',
-            in2 = fastq_dir+'/'+sample_id+'_2.fastq',
-            sample_id = sample_id
-        }
-    }
-    
-
-    # output {
-    #     File clean_out1 = pair_end.out1
-    #     File clean_out2 = pair_end.out2
-    #     File html_report = pair_end.html_report
-    #     File json_report = pair_end.json_report
-    # }
-
-}
-
-task pair_end {
+task fastq {
 
     input {
         
@@ -48,9 +22,10 @@ task pair_end {
         String report_title = "\'fastp report\'"
 
         # excute env
-        Int cpu = 2
-        String memory = "4G"
-        String disks = "local-disk 50 cloud_ssd"
+		String docker
+		String cluster_config
+		String disk_size
+		
 
     }
 
@@ -61,28 +36,28 @@ task pair_end {
 
         # basic command
         /opt/conda/bin/fastp \
-        --in1 ~{in1} \
-        --in2 ~{in2} \
-        --out1 ~{out1_name} \
-        --out2 ~{out2_name} \
-        --json ~{json} \
-        --html ~{html} \
-        --report_title ~{report_title} \
+        --in1 ${in1} \
+        --in2 ${in2} \
+        --out1 ${out1_name} \
+        --out2 ${out2_name} \
+        --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 }
+        ${ 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 }
 
     >>>
 
     runtime {
-        cpu: cpu
-        memory: memory
-        disks: disks
-        docker: "registry-vpc.cn-shanghai.aliyuncs.com/easygene/fastp:v0.20.1_cv1"
+		docker:docker
+		cluster:cluster_config
+		systemDisk:"cloud_ssd 40"
+		dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
     }
 
     output {