更新 'tasks/CNVkit.wdl'

tasks/CNVkit.wdl

@@ -5,7 +5,6 @@ task cnvkit{
     String? fasta
     File ref_flat
     File bed_file
-    String method
     File hrd
     File tumor_bam
     File tumor_bam_index
@@ -36,7 +35,7 @@ task cnvkit{
        if [ ${normal_bam} ]; then   
                /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} \
                   --normal ${normal_bam} \
-                  --method ${method} \
+                  --method wgs \
                   --fasta ${ref_dir} \
                   --annotate ${ref_flat} -p $nt \
                   --drop-low-coverage \
@@ -46,7 +45,7 @@ task cnvkit{
     	       # Prepare the target bed
                #/root/miniconda2/bin/cnvkit.py --annotate ${ref_flat} --split --short-names -o my_baits.bed
                
-               /root/miniconda2/bin/cnvkit.py autobin ${tumor_bam} --method ${method} -g access.bed
+               /root/miniconda2/bin/cnvkit.py autobin ${tumor_bam} --method wgs -g access.bed
                
                /root/miniconda2/bin/cnvkit.py coverage ${tumor_bam} ${sample}.target.bed -o ${sample}.T.targetcoverage.cnn
                /root/miniconda2/bin/cnvkit.py coverage ${tumor_bam} ${sample}.antitarget.bed -o ${sample}.T.antitargetcoverage.cnn