更新 'tasks/HRD.wdl'

tasks/HRD.wdl

@@ -8,6 +8,7 @@ task HRD {
   File tumor_bam_index
   File? normal_bam
   File? normal_bam_index
+  File? bed_file
   String docker
   String cluster_config
   String disk_size
@@ -21,16 +22,23 @@ task HRD {
     small=${sample}'.small.seqz.gz'
     
     # bam2seqz
-    sequenza-utils bam2seqz -gc ${gc} --fasta ${ref_dir}/${fasta} -n ${normal_bam} -t ${tumor_bam} -o $seqz -C chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY --parallel 24
                 
+    if [ ${normal_bam} ]; then
+    	sequenza-utils bam2seqz -gc ${gc} --fasta ${ref_dir}/${fasta} -n ${normal_bam} -t ${tumor_bam} -o $seqz -C chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY --parallel 24
+    else
+        sequenza-utils bam2seqz -gc ${gc} --fasta ${ref_dir}/${fasta} -t ${tumor_bam} -o $seqz -C chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY --parallel 24
+    fi
     # merge and remove
     zcat ${sample}_*.seqz.gz | awk '{if (NR == 1 || (NR != 1 && $1 != "chromosome")) {print $0}}' | bgzip > $seqz
     tabix -f -s 1 -b 2 -e 2 -S 1 $seqz
     rm ${sample}_*.seqz.gz; rm ${sample}_*.seqz.gz.tbi
     
     # seqz_binning: WES: 50; WGS: 200
-    sequenza-utils seqz_binning --seqz $seqz -w 200 -o $small
-    
+    if [ ${bed_file} ]; then
+    	sequenza-utils seqz_binning --seqz $seqz -w 50 -o $small
+    else
+        sequenza-utils seqz_binning --seqz $seqz -w 200 -o $small
+    fi
     # analysis in r
     Rscript /home/sequenza/sequenza.r '.' ${sample} 'XY'
   >>>