更新 'tasks/spladder_merge.wdl'

tasks/spladder_merge.wdl

@@ -15,9 +15,11 @@ task spladder_merge {
         set -e
 
         mkdir -p ${sample_id}/spladder_out/spladder
-                  
-        ls ${bam} | grep bam$ > alignment.txt
-        ls ${bam} | grep bai$ > alignment_bai.txt
+        
+        ln -s ${bam}/*.bam$ ./                  
+        ls ./ | grep bam$ > alignment.txt
+        ln -s ${bam}/*.bai$ ./           
+        ls ./ | grep bai$ > alignment_bai.txt
         ln -s ${pickle}/*.pickle ${sample_id}/spladder_out/spladder/
         ls ${sample_id}/spladder_out/spladder/ >> pickle.txt