更新 'tasks/CNVkit.wdl'

tasks/CNVkit.wdl

@@ -13,27 +13,28 @@ task cnvkit{
     String disk_size
 
     command <<<
+
         set -o pipefail
         set -e
 
-        cnvkit.py batch ${tumor_bam} -n ${normal_bam} -m wgs -f ${ref_dir}/${fasta} --annotate ${ref_flat}
+        /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} -n ${normal_bam} -m wgs -f ${ref_dir}/${fasta} --annotate ${ref_flat}
 
-        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
 
-        cnvkit.py diagram ${sample}.cnr -s ${sample}.call.cns -o ${sample}.diagram.pdf
+        /root/miniconda2/bin/cnvkit.py diagram ${sample}.cnr -s ${sample}.call.cns -o ${sample}.diagram.pdf
 
-        cnvkit.py heatmap ${sample}.cnr ${sample}.call.cns -o ${sample}.heatmap.pdf
+        /root/miniconda2/bin/cnvkit.py heatmap ${sample}.cnr ${sample}.call.cns -o ${sample}.heatmap.pdf
 
-        cnvkit.py genemetrics ${sample}.cnr -t 0.2 -m 3 -o ${sample}.ratio_cnv.txt
+        /root/miniconda2/bin/cnvkit.py genemetrics ${sample}.cnr -t 0.2 -m 3 -o ${sample}.ratio_cnv.txt
 
-        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}.call.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
         comm -12 ratio_cnv.txt segment_cnv.txt > ${sample}.trusted_genes.txt
 
         awk 'NR==FNR {a[$1]=$2;next} NR!=FNR {if(FNR == 1 || (FNR != 1 && $1 in a)) print $0}' ${sample}.trusted_genes.txt ${sample}.ratio_cnv.txt > ${sample}.ratio_cnv.trusted.txt
-        cnvkit.py call ${sample}.ratio_cnv.trusted.txt -m threshold -o ${sample}.ratio_cnv.call.txt
+        /root/miniconda2/bin/cnvkit.py call ${sample}.ratio_cnv.trusted.txt -m threshold -o ${sample}.ratio_cnv.call.txt
         awk '{if ($6 != 2) print $0}' ${sample}.ratio_cnv.call.txt > ${sample}.ratio_cnv.call.filter.txt
 
         ls ./