更新 'tasks/battenberg.wdl'

tasks/battenberg.wdl

@@ -12,12 +12,16 @@ task battenberg {
 
         set -o pipefail
         set -e
-        samtools view -h ${normal_bam} |sed 's/chr//g'|samtools view  -bS > ./${normal_id}.sorted.deduped.nochr.bam
-        samtools view -h ${tumor_bam} |sed 's/chr//g'|samtools view  -bS > ./${sample_id}.sorted.deduped.nochr.bam
+        cp ${normal_bam} ./${normal_id}.bam
+        cp ${tumor_bam} ./${sample_id}.bam
+        samtools view -h ./${normal_id}.bam |sed 's/chr//g'|samtools view  -bS > ./${normal_id}.sorted.deduped.nochr.bam
+        samtools view -h ./${sample_id}.bam |sed 's/chr//g'|samtools view  -bS > ./${sample_id}.sorted.deduped.nochr.bam
+      
+     
         samtools index  ./${normal_id}.sorted.deduped.nochr.bam
         samtools index  ./${sample_id}.sorted.deduped.nochr.bam
         cp /opt/battenberg_reference/battenberg_wgs.R ./
-        Rscript ./battenberg_wgs.R -t ${sample_id} -n ${normal_id} --nb ${normal_id}.sorted.deduped.nochr.bam --tb  ${sample_id}.sorted.deduped.nochr.bam --cpu 4 --sex female -o ./
+        Rscript ./battenberg_wgs.R -t ${sample_id} -n ${normal_id} --nb ./${normal_id}.sorted.deduped.nochr.bam --tb  ./${sample_id}.sorted.deduped.nochr.bam --cpu 4 --sex female -o ./
         mkdir ${sample_id}_chr_png
         cp ${sample_id}_subclones_chr*.png ./${sample_id}_chr_png/
         tar zcvf ./${sample_id}_chr_png.tgz ./${sample_id}_chr_png/