Fixbug: insert size in Pindel

tasks/Pindel.wdl

@@ -24,12 +24,18 @@ task Pindel {
     
     samtools index -@ 4 ./input/$bam_file_name
     
-    java "-Xmx16G" -jar /software/picard/picard.jar  CollectInsertSizeMetrics \
+    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/${sample_id}_picard.txt|sed -n '8p'|cut -f 6|cut -d . -f 1`
+    temp_mean_insert_size=`cat pindel_result/${sample_id}_picard.txt|sed -n '8p'|cut -f 6|cut -d . -f 1`
+    if [ $temp_mean_insert_size -lt 151 ];then
+      mean_insert_size=151
+    else
+      mean_insert_size=`echo $temp_mean_insert_size`
+    fi
+    
     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