更新 'tasks/spladder.wdl'

tasks/spladder.wdl

@@ -23,13 +23,31 @@ task spladder {
 		done                  
 
         sed ':a ; N;s/\n/,/ ; t a ; ' bam.txt > alignment.txt
-        
+          
+        for i in ${sep=" " bai}
+		do
+        echo $i >> bai.txt
+		done                  
+
+        sed ':a ; N;s/\n/,/ ; t a ; ' bai.txt > alignment_bai.txt
+          
         for i in ${sep=" " pickle}
 		do
         ln -s $i ${sample_id}/spladder_out/spladder/
         ls ${sample_id}/spladder_out/spladder/ >> pickle.txt
 		done
-
+		
+		spladder build -o ${sample_id}/spladder_out \
+          --annotation ${reference_gtf_file} \
+          --bams alignment.txt \
+          --confidence 2 \
+          --merge-strat merge_graphs \
+          --validate-sg \
+          --readlen 150 \
+          --parallel 4 \
+          --event-types exon_skip,intron_retention,alt_3prime,alt_5prime,mutex_exons,mult_exon_skip
+          
+          
         find . -depth > fileList.txt
     >>>
 
@@ -43,6 +61,13 @@ task spladder {
     output {
         File fileList = "fileList.txt"
         File alignment = "alignment.txt"
+        File alignment_bai = "alignment_bai.txt"
         File pickle_txt = "pickle.txt"
+        Array[File] AS_gff = glob("${sample_id}/spladder_out/*.gff3")
+        Array[File] AS_pickle = glob("${sample_id}/spladder_out/*.pickle")
+        Array[File] AS_gz = glob("${sample_id}/spladder_out/*.gz")
+        Array[File] AS_hdf5 = glob("${sample_id}/spladder_out/*.hdf5")
+        Array[File] spladder = glob("${sample_id}/spladder_out/spladder/*")
+        Array[File] tmp = glob("${sample_id}/spladder_out/tmp/*")
     }
 }