Update 'tasks/spladder_EC.wdl'

tasks/spladder_EC.wdl

@@ -7,6 +7,7 @@ task spladder_EC {
     File reference_gtf_file
     File samples
     File merge_count_hdf5
+    File pickle_list
     
     String event_types
     String spladder_docker
@@ -26,13 +27,13 @@ task spladder_EC {
         ln -s ${bam}/*.bai ./
         cat ${samples} | while read a; do ls ./ | grep bai$ | grep $a; done > alignment_bai.txt
 
-        cp -r ${pickle}/*.pickle ${sample_id}/spladder_out/spladder/
+        cat ${pickle_list}| while read a; do ln -s $a ${sample_id}/spladder_out/spladder/; done 
         cat ${samples} | while read a; do ls ${sample_id}/spladder_out/spladder/| grep pickle$| grep $a; done >> pickle.txt
 		
         cp -r ${merge_graphs} ${sample_id}/spladder_out/spladder/
         cp -r ${merge_count_hdf5} ${sample_id}/spladder_out/spladder/ 
 
-        cp -r ${count_hdf5}/*.hdf5 ${sample_id}/spladder_out/spladder/
+        ln -s ${count_hdf5}/*.hdf5 ${sample_id}/spladder_out/spladder/
         cat ${samples} | while read a; do ls ${sample_id}/spladder_out/spladder/| grep hdf5$| grep $a; done >> count_hdf5.txt