更新 'tasks/spladder.wdl'

tasks/spladder.wdl

@@ -10,13 +10,12 @@ task spladder {
     String cluster
     String disk_size
 
-
     
     command <<<
         set -o pipefail
         set -e
 
-        mkdir -p ${sample_id}/spladder_out
+        mkdir -p ${sample_id}/spladder_out/spladder
                   
         for i in ${sep=" " bam}
 		do
@@ -27,9 +26,8 @@ task spladder {
         
         for i in ${sep=" " pickle}
 		do
-        ln -s $i ${sample_id}/spladder_out/$i
-        echo ${sample_id}/spladder_out/$i
-        echo ${sample_id}/spladder_out/$i >> pickle.txt
+        ln -s $i ${sample_id}/spladder_out/spladder/
+        ls ${sample_id}/spladder_out/spladder/ >> pickle.txt
 		done
 
         find . -depth > fileList.txt