上传文件至 'tasks'

tasks/tmb.wdl

+task TMB {
+  
+  String sample
+  File hg38_CDS
+  File regions
+  File snpindel_txt
+  String docker
+  String cluster_config
+  String disk_size
+  Boolean AF_filter
+  
+  command <<<
+    set -o pipefail
+    set -e
+    nt=$(nproc)
+    
+    if [ ${regions} ];then
+        sort -k1,1 -k2,2n ${regions} | bedtools merge -i - > merged.bed
+        bedtools intersect -a merged.bed -b ${hg38_CDS} > merged_intersect.bed
+        size=`awk -F'\t' 'BEGIN{SUM=0}{SUM+=$3-$2}END{print SUM}' merged_intersect.bed`
+    else
+        size=`awk -F'\t' 'BEGIN{SUM=0}{SUM+=$3-$2}END{print SUM}' ${hg38_CDS}`
+    fi 
+    
+    # analysis in python
+    if ${AF_filter};then
+        python ~/tmb.py ${snpindel_txt} $size ${sample} 'yes'
+    else
+        python ~/tmb.py ${snpindel_txt} $size ${sample} 'no'
+    fi
+
+  >>>
+  
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  
+  output {
+    File snp_indel="${sample}.snp_indel.txt"
+    File tmb="${sample}.TMB.txt"
+  }
+}