first commit

defaults

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+{   
+    "disk_size":"200",
+    "filter_vep_annovar_docker":"registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/filter_vep_charger_py:v1",
+    "filter_vep_annovar_cluster":"OnDemand bcs.ps.r.xlarge img-ubuntu-vpc"
+}

inputs

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+{
+    "{{ project_name }}.sample_id": "{{ sample_id }}",
+    "{{ project_name }}.vep_vcf": "{{ vep_vcf }}",
+    "{{ project_name }}.annovar_txt": "{{ annovar_txt }}",
+    "{{ project_name }}.disk_size": "{{ disk_size }}",
+    "{{ project_name }}.filter_vep_annovar_docker": "{{ filter_vep_annovar_docker }}",
+    "{{ project_name }}.filter_vep_annovar_cluster": "{{ filter_vep_annovar_cluster }}"
+}

tasks/filter_vep_annovar.wdl

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+task filter_vep_annovar{
+    String sample_id
+    File vep_vcf
+    File annovar_txt
+
+    String disk_size
+    String docker
+    String cluster
+
+    command <<<
+	
+        set -o pipefail
+        set -e
+
+        mkdir ./output/
+        mkdir ./prepare/
+ 
+        vep_index=`echo ${vep_vcf}|awk -F "/" '{print $NF}'`
+        vep_id=`echo ${vep_vcf}|awk -F "/" '{print $NF}'|sed 's/\.vcf//'`
+        
+        echo ${sample_id}
+        sed '1,1000s/^#CHROM/CHROM/' ${vep_vcf} |grep  -v "#"  > prepare/$vep_id.noheader.vcf
+        python /software/filter_dot.py --vep_vcf prepare/$vep_id.noheader.vcf
+        sed '1,1000s/^#CHROM/CHROM/' ${vep_vcf} |grep  "#" > prepare/$vep_id.header.nodot.vcf
+        sed '1s/^CHROM/#CHROM/' prepare/$vep_id.noheader.nodot.vcf  >> prepare/$vep_id.header.nodot.vcf
+        perl /software/convert2annovar.pl -format vcf4 ./prepare/$vep_id.header.nodot.vcf  -outfile prepare/$vep_index.avinput -allsample -withfreq -include
+        
+        echo "uid" > ./prepare/$vep_index.avinput_uid.txt
+        cut -f 1-5 prepare/$vep_index.avinput | sed 's/\t/_/g' >> prepare/$vep_index.avinput_uid.txt
+        paste prepare/$vep_index.avinput_uid.txt prepare/$vep_id.noheader.nodot.vcf > prepare/$vep_index.add_uid.txt
+        Rscript /software/filter.R  --vep_file prepare/$vep_index.add_uid.txt --annovar_file ${annovar_txt}
+        python /software/filter.py --uid_list prepare/annovar_uid.txt --vep_vcf prepare/$vep_index.add_uid.txt
+        sed '1,1000s/^#CHROM/CHROM/'  ./prepare/$vep_id.header.nodot.vcf |grep  "#"  > output/$vep_id.filter.vcf
+        sed '1s/^CHROM/#CHROM/' prepare/$vep_id.filter_prepare.vcf >> output/$vep_id.filter.vcf
+        rm output/$vep_id.removed.vcf
+ 
+    >>>
+	
+    runtime {
+        docker: docker
+        cluster: cluster
+        systemDisk: "cloud_ssd 40"
+        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output {
+        Array[File] filter_result=glob("./output/${sample_id}*")
+    }
+
+}
+
+

workflow.wdl

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+import "./tasks/filter_vep_annovar.wdl" as filter_vep_annovar
+
+workflow {{ project_name }} {
+    String sample_id
+    File vep_vcf
+    File annovar_txt
+
+    String disk_size
+    String filter_vep_annovar_docker
+    String filter_vep_annovar_cluster
+
+
+        call filter_vep_annovar.filter_vep_annovar as filter_vep_annovar {
+                input:	
+                sample_id=sample_id,
+                vep_vcf=vep_vcf,
+                annovar_txt=annovar_txt,
+                disk_size=disk_size,
+                docker=filter_vep_annovar_docker,
+                cluster=filter_vep_annovar_cluster
+        }
+
+
+}	
+