fix(CNVkit): output

tasks/CNVkit.wdl

@@ -19,10 +19,6 @@ task CNVkit {
     set -e
     nt=$(nproc)
     
-    CNV_ANALYSIS_PATH=/cromwell_root/tmp/cnvkit
-    mkdir -p $CNV_ANALYSIS_PATH
-    cd $CNV_ANALYSIS_PATH
-    
     cnvkit.py access ${ref_dir}/${fasta} -o access.bed
     # Prepare the target bed
     cnvkit.py target ${regions} --annotate ${ref_flat} --split --short-names -o my_baits.bed
@@ -69,8 +65,8 @@ task CNVkit {
     cnvkit.py genemetrics ${sample}.cnr -s ${sample}.call.cns -t 0.2 -m 3 -o ${sample}.segment-genes.txt
     cat ${sample}.ratio-genes.txt | tail -n+2 | cut -f1 | sort | uniq > ratio-genes.txt
     cat ${sample}.segment-genes.txt | tail -n+2 | cut -f1 | sort | uniq > segment-genes.txt
-    comm -12 ratio-genes.txt segment-genes.txt > trusted_cnv_genes.txt
-    for gene in `cat trusted_cnv_genes.txt`
+    comm -12 ratio-genes.txt segment-genes.txt > ${sample}.trusted_cnv_genes.txt
+    for gene in `cat ${sample}.trusted_cnv_genes.txt`
     do
       cnvkit.py scatter ${sample}.cnr -s ${sample}.call.cns -g $gene -o ./gainloss/${sample}.$gene.scatter.pdf
     done
@@ -92,7 +88,7 @@ task CNVkit {
     File stats = "${sample}.stats"
     File call_cns = "${sample}.call.cns"
     File genemetrics = "${sample}.cnv.txt"
-    File gainloss_genes = "/cromwell_root/tmp/cnvkit/trusted_cnv_genes.txt"
-    Array[File] gainloss = glob("/cromwell_root/tmp/cnvkit/gainloss/*")
+    File gainloss_genes = "${sample}.trusted_cnv_genes.txt"
+    Array[File] gainloss = glob("./gainloss/*")
   }
 }