更新 'tasks/CNVkit.wdl'

tasks/CNVkit.wdl

@@ -12,22 +12,23 @@ task cnvkit{
     String cluster_config
     String disk_size
 
+
     command <<<
 
         set -o pipefail
         set -e
 
-        /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} -n ${normal_bam} -m wgs -f ${ref_dir} --annotate ${ref_flat}
+        /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} -n ${normal_bam} -m wgs -f ${ref_dir} --annotate ${ref_flat} --diagram --scatter
 
-        /root/miniconda2/bin/cnvkit.py scatter ${sample}.cnr -s ${sample}.cns -o ${sample}_scatter.pdf
+        #/root/miniconda2/bin/cnvkit.py scatter ${sample}.cnr -s ${sample}.cns -o ${sample}_scatter.pdf
 
-        /root/miniconda2/bin/cnvkit.py diagram ${sample}.cnr -s ${sample}.call.cns -o ${sample}.diagram.pdf
+        #/root/miniconda2/bin/cnvkit.py diagram ${sample}.cnr -s ${sample}.cns -o ${sample}.diagram.pdf
 
-        /root/miniconda2/bin/cnvkit.py heatmap ${sample}.cnr ${sample}.call.cns -o ${sample}.heatmap.pdf
+        /root/miniconda2/bin/cnvkit.py heatmap ${sample}.cnr ${sample}.cns -o ${sample}.heatmap.pdf
 
         /root/miniconda2/bin/cnvkit.py genemetrics ${sample}.cnr -t 0.2 -m 3 -o ${sample}.ratio_cnv.txt
 
-        /root/miniconda2/bin/cnvkit.py genemetrics ${sample}.cnr -s ${sample}.call.cns -t 0.2 -m 3 -o ${sample}.segment_cnv.txt
+        /root/miniconda2/bin/cnvkit.py genemetrics ${sample}.cnr -s ${sample}.cns -t 0.2 -m 3 -o ${sample}.segment_cnv.txt
 
         cat ${sample}.ratio_cnv.txt | tail -n+2 | cut -f1 | sort | uniq > ratio_cnv.txt
         cat ${sample}.segment_cnv.txt | tail -n+2 | cut -f1 | sort | uniq > segment_cnv.txt