更新 'tasks/spladder_merge.wdl'

tasks/spladder_merge.wdl

@@ -3,7 +3,7 @@ task spladder_merge {
     File bam
     File pickle
     File reference_gtf_file
-    
+    File samples
 
     String docker
     String cluster
@@ -16,12 +16,14 @@ task spladder_merge {
 
         mkdir -p ${sample_id}/spladder_out/spladder
         
-        ln -s ${bam}/*.bam ./                  
-        ls ./ | grep bam$ > alignment.txt
-        ln -s ${bam}/*.bai ./           
-        ls ./ | grep bai$ > alignment_bai.txt
+        ln -s ${bam}/*.bam ./
+        cat ${samples} | while read a; do ls ./ | grep bam$ | grep $a; done > alignment.txt
+       
+        ln -s ${bam}/*.bai ./
+        cat ${samples} | while read a; do ls ./ | grep bai$ | grep $a; done > alignment_bai.txt
+
         ln -s ${pickle}/*.pickle ${sample_id}/spladder_out/spladder/
-        ls ${sample_id}/spladder_out/spladder/ >> pickle.txt
+        cat ${samples} | while read a; do ls ${sample_id}/spladder_out/spladder/ | grep $a; done >> pickle.txt
 		
         nt=$(nproc)
           
@@ -32,7 +34,6 @@ task spladder_merge {
           --merge-strat merge_graphs \
           --readlen 150 \
           --parallel $nt \
-          --pyproc\
           --event-types exon_skip
           
         find . -depth > fileList.txt