更新 'tasks/CNVkit.wdl'

tasks/CNVkit.wdl

@@ -33,21 +33,20 @@ task cnvkit{
        ls ./
        
         
-       /root/miniconda2/bin/cnvkit.py batch  ${tumor_bam} \
-                  -r ${sample}.reference.cnn \
-                  --output-dir ${sample}.sampleid.cns \
-                  -p $nt
+       #/root/miniconda2/bin/cnvkit.py batch  ${tumor_bam} \
+       #           -r ${sample}.reference.cnn \
+       #           --output-dir ${sample}.sampleid.cns \
+       #           -p $nt
                   
-       ls ./
-       /root/miniconda2/bin/cnvkit.py call ${sample}.sampleid.cns \
-                  -o ${sample}.sampleid.call.cns
-                  
-        
+       #ls ./
+       #/root/miniconda2/bin/cnvkit.py call ${sample}.sampleid.cns \
+       #           -o ${sample}.sampleid.call.cns
                   
+                
 
         ls ./
 
-        tar cvf ${sample_id}.tar ${sample_id}*
+        tar cvf ${sample}.tar ${sample}*
 
     >>>
 
@@ -60,7 +59,7 @@ task cnvkit{
     }
 
     output{
-        File out_file = "${sample_id}.tar"
+        File out_file = "${sample}.tar"
         #File cnv_bed = "${sample}.ratio_cnv.call.filter.bed"
     }