更新 'tasks/spladder_merge.wdl'

tasks/spladder_merge.wdl

@@ -23,17 +23,17 @@ task spladder_merge {
         ln -s ${pickle}/*.pickle ${sample_id}/spladder_out/spladder/
         ls ${sample_id}/spladder_out/spladder/ >> pickle.txt
 		
-        # nt=$(nproc)
+        nt=$(nproc)
           
-        # 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 $nt \
-        #   --event-types exon_skip,intron_retention,alt_3prime,alt_5prime,mutex_exons,mult_exon_skip
+        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 $nt \
+          --event-types exon_skip,intron_retention,alt_3prime,alt_5prime,mutex_exons,mult_exon_skip
           
         find . -depth > fileList.txt
     >>>
@@ -51,5 +51,10 @@ task spladder_merge {
         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/*")
     }
 }