Alter: input

defaults

@@ -1,6 +1,6 @@
 {   
-    "reference":"oss://pgx-reference-data/reference/pindel/GRCh38.d1.vd1.fa",
-    "reference_fai":"oss://pgx-reference-data/reference/pindel/GRCh38.d1.vd1.fa.fai"
+    "reference":"oss://pgx-reference-data/GRCh38.d1.vd1/GRCh38.d1.vd1.fa",
+    "reference_fai":"oss://pgx-reference-data/GRCh38.d1.vd1/GRCh38.d1.vd1.fa.fai",
     "pindel_docker":"registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/pindel:0.2.5b9_3",
     "pindel_cluster":"OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
     "disk_size":"200"

tasks/pindel.wdl

@@ -1,80 +1,75 @@
-task pindel{
-    String sample_id
-    File bam
-    File reference
-    File reference_fai
+task pindel {
+  String sample_id
+  File bam
+  File reference
+  File reference_fai
 
-    String docker
-    String cluster
-    String disk_size
+  String docker
+  String cluster
+  String disk_size
 
 
-    command <<<
+  command <<<
 	
-        set -o pipefail
-        set -e
-
-        mkdir ./pindel_result/
-        mkdir ./input
-
-        cp ${bam} ./input
-
-        bam_file_name=`echo ${bam}|awk -F "/" '{print $NF}'`
-        
-        samtools index -@ 4 ./input/$bam_file_name
-        
-        java "-Xmx16G" -jar /software/picard/picard.jar  CollectInsertSizeMetrics \
-            -H ./pindel_result/${sample_id}_picard.pdf \
-            -I ./input/$bam_file_name \
-            -O ./pindel_result/${sample_id}_picard.txt
-
-        mean_insert_size=`cat pindel_result/${sample_id}_picard.txt|sed -n '8p'|cut -f 6|cut -d . -f 1`
-        bam_file_name=`echo ${bam}|awk -F "/" '{print $NF}'`
-
-        echo -e "./input/$bam_file_name\t$mean_insert_size\t${sample_id}" > ${sample_id}_config.txt
-
-        pindel -i ${sample_id}_config.txt \
-            -f ${reference} \
-            -o ./pindel_result/${sample_id} \
-            -c all \
-            -T 4 \
-            -x 4 \
-            -l \
-            -B 0 \
-            -M 3 \
-            -J /software/picard/hg38_ucsc_centromere.bed
-
-        grep "ChrID" pindel_result/${sample_id}_SI > pindel_result/${sample_id}_all_indel
-        grep "ChrID" pindel_result/${sample_id}_D >> pindel_result/${sample_id}_all_indel
-
-        awk -v chrID="chr1" '$8==chrID {print}' pindel_result/${sample_id}_all_indel > pindel_result/${sample_id}_indel
-        
-        for i in `seq 2 22`  X Y M
-            do
-                awk -v chrID=chr$i '$8==chrID {print}' pindel_result/${sample_id}_all_indel >> pindel_result/${sample_id}_indel
-            done
-
-        pindel2vcf  -r ${reference} \
-            -R GRCh38.d1.vd1 \
-            -d GDC \
-            -p pindel_result/${sample_id}_indel \
-            -v pindel_result/${sample_id}.pindel.indel.vcf
-        
-
-
-    >>>
+    set -o pipefail
+    set -e
+
+    mkdir ./pindel_result/
+    mkdir ./input
+
+    cp ${bam} ./input
+
+    bam_file_name=`echo ${bam}|awk -F "/" '{print $NF}'`
+    
+    samtools index -@ 4 ./input/$bam_file_name
+    
+    java "-Xmx16G" -jar /software/picard/picard.jar  CollectInsertSizeMetrics \
+      -H ./pindel_result/${sample_id}_picard.pdf \
+      -I ./input/$bam_file_name \
+      -O ./pindel_result/${sample_id}_picard.txt
+
+    mean_insert_size=`cat pindel_result/${sample_id}_picard.txt|sed -n '8p'|cut -f 6|cut -d . -f 1`
+    bam_file_name=`echo ${bam}|awk -F "/" '{print $NF}'`
+
+    echo -e "./input/$bam_file_name\t$mean_insert_size\t${sample_id}" > ${sample_id}_config.txt
+
+    pindel -i ${sample_id}_config.txt \
+      -f ${reference} \
+      -o ./pindel_result/${sample_id} \
+      -c all \
+      -T 4 \
+      -x 4 \
+      -l \
+      -B 0 \
+      -M 3 \
+      -J /software/picard/hg38_ucsc_centromere.bed
+
+    grep "ChrID" pindel_result/${sample_id}_SI > pindel_result/${sample_id}_all_indel
+    grep "ChrID" pindel_result/${sample_id}_D >> pindel_result/${sample_id}_all_indel
+
+    awk -v chrID="chr1" '$8==chrID {print}' pindel_result/${sample_id}_all_indel > pindel_result/${sample_id}_indel
+    
+    for i in `seq 2 22`  X Y M
+      do
+        awk -v chrID=chr$i '$8==chrID {print}' pindel_result/${sample_id}_all_indel >> pindel_result/${sample_id}_indel
+      done
+
+    pindel2vcf  -r ${reference} \
+      -R GRCh38.d1.vd1 \
+      -d GDC \
+      -p pindel_result/${sample_id}_indel \
+      -v pindel_result/${sample_id}.pindel.indel.vcf
+    
+  >>>
 	
-    runtime {
-        docker : docker
-        cluster : cluster
-        systemDisk: "cloud_ssd 40"
-        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/
-    }
-
-    output {
-        Array[File] pindel_result=glob("./pindel_result/${sample_id}*")
-    }
-
-}
-
-
+  runtime {
+    docker: docker
+    cluster: cluster
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+
+  output {
+    Array[File] pindel_result = glob("./pindel_result/${sample_id}*")
+  }
+}

workflow.wdl

@@ -1,22 +1,18 @@
 import "./tasks/pindel.wdl" as pindel
 
 workflow run_pindel {
-    String sample_id
-    File bam
-    File reference
-    File reference_fai
-
-    String pindel_docker
-
-        call pindel.pindel as pindel {
-                input:	
-                sample_id=sample_id,
-                bam=bam,
-                reference=reference,
-                reference_fai=reference_fai,
-                docker=pindel_docker
-        }
-
-
-}	
+  String sample_id
+  File bam
+  File reference
+  File reference_fai
+  String pindel_docker
 
+  call pindel.pindel as pindel {
+    input:	
+    sample_id=sample_id,
+    bam=bam,
+    reference=reference,
+    reference_fai=reference_fai,
+    docker=pindel_docker
+  }
+}