bug

pipeline.wdl

@@ -25,18 +25,13 @@ workflow pipeline {
     String project
     String cancer
 
-    String bed="/home/zhangchao/project/pipeline/workflow/script/public/bed/${probe}.bed"
+    String bed="$WORKFLOW/${probe}.bed"
     String ref = "/home/install/ref/hg19/hg19.fa"
 
     String workdir="${output_dir}"
 
     Map[String, Boolean] catecode
 
-    #    call mytask.create_dir as create_dir {
-    #        input:
-    #            workdir=workdir
-    #    }
-
     call qc.qc as qc {
         input:
             run=catecode['addQc'],

soft_bash

@@ -1,13 +1,13 @@
 # 目录环境
 export WORKFLOW=$(dirname "$(readlink -f "${BASH_SOURCE[0]}")")
-export PUBLIC=$WORKFLOW/script/public
+export PUBLIC=$WORKFLOW/codes/public
 export DATABASE=$WORKFLOW/database
 
-# python
-export PATH=/home/install/product/workflow/software/Python-3.8.11/bin:$PATH
-
 # script
 export PATH=$WORKFLOW/codes:$PATH
 
 # software
 export PATH=$WORKFLOW/software/bin:$PATH
+
+# python
+export PATH=/home/install/product/workflow/software/Python-3.8.11/bin:$PATH