Update 'tasks/spladder_EC.wdl'

tasks/spladder_EC.wdl

@@ -32,8 +32,8 @@ task spladder_EC {
         cp -r ${merge_graphs} ${sample_id}/spladder_out/spladder/
         cp -r ${merge_count_hdf5} ${sample_id}/spladder_out/spladder/ 
 
-        cp -r ${count_hdf5}/* ${sample_id}/spladder_out/spladder/
-        cat ${samples} | while read a; do ls ${sample_id}/spladder_out/spladder/| grep count| grep $a; done >> count.txt
+        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
 
 
         nt=$(nproc)
@@ -64,10 +64,9 @@ task spladder_EC {
         File alignment = "alignment.txt"
         File alignment_bai = "alignment_bai.txt"
         File pickle_txt = "pickle.txt"
-        File count_hdf5_txt = "count.txt"
+        File count_hdf5_txt = "count_hdf5.txt"
         Array[File] AS_gff = glob("${sample_id}/spladder_out/*.gff3")
         Array[File] AS_gz = glob("${sample_id}/spladder_out/*.gz")
         Array[File] spladder_out = glob("${sample_id}/spladder_out/*")
-        Array[File] spladder = glob("${sample_id}/spladder_out/spladder/*")
     }
 }