更新 'tasks/HRD.wdl'

tasks/HRD.wdl

@@ -21,8 +21,7 @@ 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
-    sequenza-utils bam2seqz -gc ${gc} --fasta ${ref_dir}/${fasta} -n ${normal_bam} -t ${tumor_bam} -o $seqz --parallel $nt
+    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
@@ -33,7 +32,7 @@ task HRD {
     sequenza-utils seqz_binning --seqz $seqz -w 200 -o $small
     
     # analysis in r
-    Rscript /home/sequenza/sequenza.r '.' ${sample}
+    Rscript /home/sequenza/sequenza.r '.' ${sample} 'XY'
   >>>
   
   runtime {