Update 'tasks/spladder_EC.wdl'

tasks/spladder_EC.wdl

@@ -27,13 +27,13 @@ task spladder_EC {
         ln -s ${bam}/*.bai ./
         cat ${samples} | while read a; do ls ./ | grep bai$ | grep $a; done > alignment_bai.txt
 
-        cat ${pickle_list}| while read a; do cp -r ${pickle}/$a ${sample_id}/spladder_out/spladder/; done 
+        cat ${pickle_list}| while read a; do ln -s ${pickle}/$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
 
 
@@ -42,10 +42,9 @@ task spladder_EC {
         spladder build -o ${sample_id}/spladder_out \
           --annotation ${reference_gtf_file} \
           --bams alignment.txt \
+          --parallel $nt \
           --confidence 2 \
-          --merge-strat merge_graphs \
           --readlen 150 \
-          --parallel $nt \
           --event-types ${event_types}