更新 'tasks/featureCounts.wdl'

tasks/featureCounts.wdl

@@ -1,29 +1,28 @@
-task featureCounts {
-    File bam_file
-    File lnc_gtf_file = "lncRNAKB_hg38_v7.gtf"
-    String gtf_dir = "oss://pgx-reference-data/reference/subread/"
-    String sample_id
-    String docker
-    String cluster
-    Int cpu_num = 4
-    Int strand_information = 0
-
-    
-    command <<<
-        mkdir -p $sample_id
-        featureCounts -T $cpu_num -t exon -g gene_id -a $gtf_dir/$lnc_gtf_file -s $strand_information -p -o $sample_id/$sample_id.genefeaturecount.txt $bam_file
-    >>>
-
-    runtime {
-        docker: docker
-        cluster: cluster
-        systemDisk: "cloud_ssd 40"
-        dataDisk: "cloud_ssd 200 /cromwell_root/"
-    }
-
-    output {
-        File out_profile = "${sample_id}.genefeaturecount.txt"
-        File out_summary = "${sample_id}.summary"
-    }
-}
-
+task featureCounts {
+    File bam_file
+    File lnc_gtf_file = "lncRNAKB_hg38_v7.gtf"
+    String gtf_dir = "oss://pgx-reference-data/reference/subread/"
+    String sample_id
+    String docker
+    String cluster
+    Int cpu_num = 4
+    Int strand_information = 0
+
+    
+    command <<<
+        featureCounts -T $cpu_num -t exon -g gene_id -a $gtf_dir/$lnc_gtf_file -s $strand_information -p -o $sample_id.genefeaturecount.txt $bam_file
+    >>>
+
+    runtime {
+        docker: docker
+        cluster: cluster
+        systemDisk: "cloud_ssd 40"
+        dataDisk: "cloud_ssd 200 /cromwell_root/"
+    }
+
+    output {
+        File out_profile = "${sample_id}.genefeaturecount.txt"
+        File out_summary = "${sample_id}.summary"
+    }
+}
+