更新 'tasks/spladder_merge .wdl'

tasks/spladder.wdl

@@ -1,69 +0,0 @@
-task spladder {
-    String sample_id
-    Array[File] bam
-    Array[File] bai
-    Array[File] pickle
-    File reference_gtf_file
-    
-
-    String docker
-    String cluster
-    String disk_size
-
-    
-    command <<<
-        set -o pipefail
-        set -e
-
-        mkdir -p ${sample_id}/spladder_out/spladder
-                  
-        for i in ${sep=" " bam}
-		do
-        echo $i >> alignment.txt
-		done                  
-
-        for i in ${sep=" " bai}
-		do
-        echo $i >> alignment_bai.txt
-		done                  
-          
-        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 ${reference_gtf_file} \
-          --bams alignment.txt \
-          --confidence 2 \
-          --merge-strat merge_graphs \
-          --validate-sg \
-          --readlen 150 \
-          --parallel 4 \
-          --event-types exon_skip,intron_retention,alt_3prime,alt_5prime,mutex_exons,mult_exon_skip
-          
-          
-        find . -depth > fileList.txt
-    >>>
-
-    runtime {
-        docker: docker
-        cluster: cluster
-        systemDisk: "cloud_ssd 500"
-        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-    }
-
-    output {
-        File fileList = "fileList.txt"
-        File alignment = "alignment.txt"
-        File alignment_bai = "alignment_bai.txt"
-        File pickle_txt = "pickle.txt"
-        Array[File] AS_gff = glob("${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/*")
-    }
-}

tasks/spladder_merge .wdl

@@ -0,0 +1,58 @@
+task spladder_merge  {
+    String sample_id
+    File bam
+    File pickle
+    File reference_gtf_file
+    File samples
+    
+
+    String docker
+    String cluster
+    String disk_size
+
+    
+    command <<<
+       set -o pipefail
+        set -e
+
+        mkdir -p ${sample_id}/spladder_out/spladder
+        
+        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/
+        cat ${samples} | while read a; do ls ${sample_id}/spladder_out/spladder/ | grep $a; done >> pickle.txt
+		
+        nt=$(nproc)
+		
+		spladder build -o ${sample_id}/spladder_out \
+          --annotation ${reference_gtf_file} \
+          --bams alignment.txt \
+          --confidence 2 \
+          --merge-strat merge_graphs \
+          --readlen 150 \
+          --parallel $nt \
+          --no-extract-ase
+          
+          
+        find . -depth > fileList.txt
+    >>>
+
+    runtime {
+        docker: docker
+        cluster: cluster
+        systemDisk: "cloud_ssd 500"
+        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output {
+        File fileList = "fileList.txt"
+        File alignment = "alignment.txt"
+        File alignment_bai = "alignment_bai.txt"
+        File pickle_txt = "pickle.txt"
+        File AS_merge_pickle = glob("${sample_id}/spladder_out/spladder/genes_graph_conf2.merge_graphs.pickle")
+    }
+}