更新 'tasks/spladder_EC.wdl'

tasks/spladder_EC.wdl

@@ -1,12 +1,14 @@
 task spladder_EC {
     String sample_id
     File bam
+    File pickle
+    File merge_graphs
+    File count_hdf5
     File reference_gtf_file
-    File spladder
-	File samples
-
-
-    String event_types
+    File samples
+    File merge_count_hdf5
+    File pickle_list
+    
     String spladder_docker
     String spladder_cluster
     String disk_size
@@ -24,8 +26,14 @@ task spladder_EC {
         ln -s ${bam}/*.bai ./
         cat ${samples} | while read a; do ls ./ | grep bai$ | grep $a; done > alignment_bai.txt
 
-        cp -r ${spladder}/* ${sample_id}/spladder_out/spladder/
-        ls ${sample_id}/spladder_out/spladder/ > spladder.txt
+        cat ${pickle_list}| while read a; do cp -r ${pickle}/$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/
+        cat ${samples} | while read a; do ls ${sample_id}/spladder_out/spladder/| grep hdf5$| grep $a; done >> count_hdf5.txt
 
 
         nt=$(nproc)
@@ -36,7 +44,7 @@ task spladder_EC {
           --parallel $nt \
           --confidence 2 \
           --readlen 150 \
-          --event-types ${event_types}
+          --event-types exon_skip,intron_retention,alt_3prime,alt_5prime,mutex_exons,mult_exon_skip
           
           
         find . -depth > fileList.txt
@@ -45,19 +53,20 @@ task spladder_EC {
     runtime {
         docker: spladder_docker
         cluster: spladder_cluster
-        systemDisk: "cloud_ssd 50"
+        systemDisk: "cloud_ssd 500"
         dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-        timeout: 129600
+        timeout: 864000
     }
 
     output {
         File fileList = "fileList.txt"
         File alignment = "alignment.txt"
         File alignment_bai = "alignment_bai.txt"
-        File spladder_txt = "spladder.txt"
+        File pickle_txt = "pickle.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("${sample_id}/spladder_out/*")
-        Array[File] spladder_file = glob("${sample_id}/spladder_out/spladder/*")          
+        Array[File] spladder = glob("${sample_id}/spladder_out/spladder/*")          
     }
 }