更新 'tasks/HRD.wdl'

tasks/HRD.wdl

@@ -23,11 +23,8 @@ task HRD {
     
     # bam2seqz
                 
-    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
+    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
+
     # 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