更新 'tasks/CNVkit.wdl'

tasks/CNVkit.wdl

@@ -34,8 +34,8 @@ task cnvkit{
            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} \
+                   /usr/local/bin/cnvkit.py target ${bed_file} --annotate ${ref_flat} --split --short-names -o my_baits.bed
+                   /usr/local/bin/cnvkit.py batch ${tumor_bam} \
                       --normal ${normal_bam} \
                       --targets my_baits.bed \
                       --fasta ${ref_dir} \
@@ -44,16 +44,16 @@ task cnvkit{
                       --output-dir ${sample}.reference.cnn
            else
                    echo "WES no normal"
-                   /root/miniconda2/bin/cnvkit.py access ${ref_dir} -o access.bed
+                   /usr/local/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
+                   /usr/local/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
+                   /usr/local/bin/cnvkit.py autobin ${tumor_bam} -t my_baits.bed -g access.bed
 
-                   /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
+                   /usr/local/bin/cnvkit.py coverage ${tumor_bam} my_baits.target.bed -o ${sample}.T.targetcoverage.cnn
+                   /usr/local/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 my_baits.target.bed -a my_baits.antitarget.bed
+                   /usr/local/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         
@@ -61,7 +61,7 @@ task cnvkit{
            echo "WGS"
            if [ ${normal_bam} ]; then
                    echo "WGS with normal"
-                   /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} \
+                   /usr/local/bin/cnvkit.py batch ${tumor_bam} \
                       --normal ${normal_bam} \
                       --method wgs \
                       --fasta ${ref_dir} \
@@ -70,16 +70,16 @@ task cnvkit{
                       --output-dir ${sample}.reference.cnn
            else
                    echo "WGS no normal"
-                   /root/miniconda2/bin/cnvkit.py access ${ref_dir} -o access.bed
+                   /usr/local/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
+                   #/usr/local/bin/cnvkit.py --annotate ${ref_flat} --split --short-names -o my_baits.bed
 
-                   /root/miniconda2/bin/cnvkit.py autobin ${tumor_bam} --method wgs -g access.bed
+                   /usr/local/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
+                   /usr/local/bin/cnvkit.py coverage ${tumor_bam} ${sample}.target.bed -o ${sample}.T.targetcoverage.cnn
+                   /usr/local/bin/cnvkit.py coverage ${tumor_bam} ${sample}.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
+                   /usr/local/bin/cnvkit.py reference -o ${sample}.reference.cnn/reference.cnn -f ${ref_dir} -t ${sample}.target.bed -a ${sample}.antitarget.bed
 
            fi
        fi
@@ -87,24 +87,24 @@ task cnvkit{
        ls ./
        
         
-       /root/miniconda2/bin/cnvkit.py batch  ${tumor_bam} \
+       /usr/local/bin/cnvkit.py batch  ${tumor_bam} \
                   -r ${sample}.reference.cnn/reference.cnn \
                   --output-dir ${sample}.cns \
                   -p $nt
                   
        ls ./
-       /root/miniconda2/bin/cnvkit.py call ${sample}.cns/${sample}.cns --center-at $center \
+       /usr/local/bin/cnvkit.py call ${sample}.cns/${sample}.cns --center-at $center \
                   -o ${sample}.call.cns
                   
        
            # Plot the results
-    	/root/miniconda2/bin/cnvkit.py scatter ${sample}.cns/${sample}.cnr -s ${sample}.call.cns -o ${sample}.scatter.pdf
-    	/root/miniconda2/bin/cnvkit.py diagram ${sample}.cns/${sample}.cnr -s ${sample}.call.cns -o ${sample}.diagram.pdf
-    	/root/miniconda2/bin/cnvkit.py heatmap ${sample}.cns/${sample}.cnr ${sample}.call.cns -o ${sample}.heatmap.pdf
+    	/usr/local/bin/cnvkit.py scatter ${sample}.cns/${sample}.cnr -s ${sample}.call.cns -o ${sample}.scatter.pdf
+    	/usr/local/bin/cnvkit.py diagram ${sample}.cns/${sample}.cnr -s ${sample}.call.cns -o ${sample}.diagram.pdf
+    	/usr/local/bin/cnvkit.py heatmap ${sample}.cns/${sample}.cnr ${sample}.call.cns -o ${sample}.heatmap.pdf
        
          
         #gain and loss
-        /root/miniconda2/bin/cnvkit.py export vcf ${sample}.call.cns -y -i "${sample}" -o ${sample}.call.cns.vcf
+        /usr/local/bin/cnvkit.py export vcf ${sample}.call.cns -y -i "${sample}" -o ${sample}.call.cns.vcf
                 
 
         tar cvf ${sample}.tar ${sample}*