更新 'tasks/CNVkit.wdl'

tasks/CNVkit.wdl

@@ -29,16 +29,18 @@ task cnvkit{
                   --annotate ${ref_flat} -p $nt \
                   --targets ${bed_file} \
                   --drop-low-coverage \
-                  --output-dir ${sample_id}.reference.cnn
+                  --output-dir ${sample}.reference.cnn
+       ls ./
+       
         
        /root/miniconda2/bin/cnvkit.py batch  ${tumor_bam} \
-                  -r ${sample_id}.reference.cnn \
-                  --output-dir ${sample_id}.sampleid.cns \
+                  -r ${sample}.reference.cnn \
+                  --output-dir ${sample}.sampleid.cns \
                   -p $nt
                   
-                  
-       /root/miniconda2/bin/cnvkit.py call ${sample_id}.sampleid.cns \
-                  -o ${sample_id}.sampleid.call.cns
+       ls ./
+       /root/miniconda2/bin/cnvkit.py call ${sample}.sampleid.cns \
+                  -o ${sample}.sampleid.call.cns