revise count wdl

tasks/count.wdl

@@ -8,8 +8,7 @@ task count {
     command <<<
       mkdir -p /cromwell_root/tmp/ballgown/${sample_id}
       cp -r ${sep=" " ballgown} /cromwell_root/tmp/ballgown/${sample_id}
-      cd /cromwell_root/tmp/
-      count -g ${sample_id}_gene_count_matrix.csv -t ${sample_id}_transcript_count_matrix.csv
+      count -i /cromwell_root/tmp/ballgown -l 150 -g ${sample_id}_gene_count_matrix.csv -t ${sample_id}_transcript_count_matrix.csv
     >>>
     
     runtime {