更新 'tasks/CNVkit_raw.wdl'

tasks/CNVkit.wdl → tasks/CNVkit_raw.wdl

@@ -4,7 +4,7 @@ task cnvkit{
     File ref_dir
     String? fasta
     File ref_flat
-    # File hrd
+    File hrd
     File tumor_bam
     File tumor_bam_index
     File? normal_bam
@@ -29,8 +29,8 @@ task cnvkit{
     	/root/miniconda2/bin/cnvkit.py metrics ${sample}.cnr -s ${sample}.cns > ${sample}.stats
     
         # Derive each segment's absolute integer copy number, ploidy must be int value
-        # PURITY=`awk -F'\t' '{print $6}' ${hrd} | sed -n '2p'`
-        PURITY=3.3
+        PURITY=`awk -F'\t' '{print $6}' ${hrd} | sed -n '2p'`
+        #PURITY=3.3
         /root/miniconda2/bin/cnvkit.py segmetrics ${sample}.cnr -s ${sample}.cns --ci -o ${sample}.segmetrics.cns
         /root/miniconda2/bin/cnvkit.py call ${sample}.segmetrics.cns --drop-low-coverage --filter ci -m threshold --purity $PURITY -o ${sample}.call.cns