更新 'tasks/battenberg.wdl'

sample_id

tasks/battenberg.wdl

@@ -1,5 +1,5 @@
 task battenberg {
-    String tumor_id
+    String sample_id
     File tumor_bam
     String normal_id
     File normal_bam
@@ -13,14 +13,14 @@ 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 ${tumor_bam} |sed 's/chr//g'|samtools view  -bS > ./${tumor_id}.sorted.deduped.nochr.bam
+        samtools view -h ${tumor_bam} |sed 's/chr//g'|samtools view  -bS > ./${sample_id}.sorted.deduped.nochr.bam
         samtools index  ./${normal_id}.sorted.deduped.nochr.bam
-        samtools index  ./${tumor_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 ${tumor_id} -n ${normal_id} --nb ${normal_id}.sorted.deduped.nochr.bam --tb  ${tumor_id}.sorted.deduped.nochr.bam --cpu 10 --sex female -o ./
-        mkdir ${tumor_id}_chr_png
-        cp ${tumor_id}_subclones_chr*.png ./${tumor_id}_chr_png/
-        tar zcvf ./${tumor_id}_chr_png.tgz ./${tumor_id}_chr_png/
+        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 10 --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/
 
     >>>
 
@@ -32,16 +32,16 @@ task battenberg {
     }
 
     output {
-        File subclones = "${tumor_id}_subclones.txt"
-        File rho = "${tumor_id}_rho_and_psi.txt"
-        File average_png = "${tumor_id}_BattenbergProfile_average.png"
-        File subclones_png = "${tumor_id}_subclones.png"
-        File distance_png = "${tumor_id}_distance.png"
-        File tumor_png = "${tumor_id}.tumour.png"
-        File germline_png = "${tumor_id}.germline.png"
-        File coverage_png = "${tumor_id}_coverage.png"
-        File alleleratio_png = "${tumor_id}_alleleratio.png"
-        File chr_png = "${tumor_id}_chr_png.tgz"
+        File subclones = "${sample_id}_subclones.txt"
+        File rho = "${sample_id}_rho_and_psi.txt"
+        File average_png = "${sample_id}_BattenbergProfile_average.png"
+        File subclones_png = "${sample_id}_subclones.png"
+        File distance_png = "${sample_id}_distance.png"
+        File tumor_png = "${sample_id}.tumour.png"
+        File germline_png = "${sample_id}.germline.png"
+        File coverage_png = "${sample_id}_coverage.png"
+        File alleleratio_png = "${sample_id}_alleleratio.png"
+        File chr_png = "${sample_id}_chr_png.tgz"
     }
 
 }