更新 'tasks/CNVkit.wdl'

tasks/CNVkit.wdl

@@ -34,7 +34,9 @@ task cnvkit{
                   
        #WES
        if [ ${bed_file} ]; then
+           echo "WES"
            if [ ${normal_bam} ]; then
+                   echo "WES with normal"
                    /root/miniconda2/bin/cnvkit.py target ${bed_file} --annotate ${ref_flat} --split --short-names -o my_baits.bed
                    /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} \
                       --normal ${normal_bam} \
@@ -44,22 +46,24 @@ task cnvkit{
                       --drop-low-coverage \
                       --output-dir ${sample}.reference.cnn
            else
+                   echo "WES no normal"
                    /root/miniconda2/bin/cnvkit.py access ${ref_dir} -o access.bed
                    # Prepare the target bed
                   /root/miniconda2/bin/cnvkit.py target ${bed_file} --annotate ${ref_flat} --split --short-names -o my_baits.bed
 
                    /root/miniconda2/bin/cnvkit.py autobin ${tumor_bam} -t my_baits.bed -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
+                   /root/miniconda2/bin/cnvkit.py coverage ${tumor_bam} my_baits.target.bed -o ${sample}.T.targetcoverage.cnn
+                   /root/miniconda2/bin/cnvkit.py coverage ${tumor_bam} my_baits.antitarget.bed -o ${sample}.T.antitargetcoverage.cnn
 
-                   /root/miniconda2/bin/cnvkit.py reference -o ${sample}.reference.cnn/reference.cnn -f ${ref_dir} -t ${sample}.target.bed -a ${sample}.antitarget.bed
+                   /root/miniconda2/bin/cnvkit.py reference -o ${sample}.reference.cnn/reference.cnn -f ${ref_dir} -t my_baits.target.bed -a my_baits.antitarget.bed
            fi
     
        #WGS         
        else
-
-           if [ ${normal_bam} ]; then   
+           echo "WGS"
+           if [ ${normal_bam} ]; then
+                   echo "WGS with normal"
                    /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} \
                       --normal ${normal_bam} \
                       --method wgs \
@@ -68,6 +72,7 @@ task cnvkit{
                       --drop-low-coverage \
                       --output-dir ${sample}.reference.cnn
            else
+                   echo "WGS no normal"
                    /root/miniconda2/bin/cnvkit.py access ${ref_dir} -o access.bed
                    # Prepare the target bed
                    #/root/miniconda2/bin/cnvkit.py --annotate ${ref_flat} --split --short-names -o my_baits.bed