上传文件至 'tasks'

tasks/fastq.wdl

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+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 {
+
+    input {
+        
+        # I/O options
+        File in1
+        File in2
+        String sample_id
+
+        Boolean? phred64 = false 
+        Boolean? fix_mgi_id = false
+
+        String? adapter_sequence
+        String? adapter_sequence_r2
+
+        Int? reads_to_process # specify how many reads/pairs to be processed. Default 0 means process all reads.
+
+        # reporting options
+        String json = sample_id+"fastp.json"
+        String html = sample_id+"fastp.html"
+        String report_title = "\'fastp report\'"
+
+        # excute env
+        Int cpu = 2
+        String memory = "4G"
+        String disks = "local-disk 50 cloud_ssd"
+
+    }
+
+    String out1_name = sample_id+'clean_1.fastq'
+    String out2_name = sample_id+'clean_2.fastq'
+
+    command <<<
+
+        # basic command
+        /opt/conda/bin/fastp \
+        --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 }
+
+    >>>
+
+    runtime {
+        cpu: cpu
+        memory: memory
+        disks: disks
+        docker: "registry-vpc.cn-shanghai.aliyuncs.com/easygene/fastp:v0.20.1_cv1"
+    }
+
+    output {
+        File out1 = out1_name
+        File out2 = out2_name
+        File json_report = json
+        File html_report = html
+    }
+
+}