更新 'tasks/fastqTobam.wdl'

tasks/fastqTobam.wdl

@@ -34,7 +34,7 @@ task SentieonFastqToBam {
         export SENTIEON_LICENSE=${SENTIEON_LICENSE}
         nt=$(nproc)
         
-        sentieon bwa mem -R -R "@RG\tID:${sample_id}\tSM:${sample_id}\tPL:${Seq_platform}" ${bwa_args} -K ${bwa_chunk_size} -t $nt ${ref_fasta_dir}/${ref_fasta} ${fastq1} ${fastq2} \
+        sentieon bwa mem -R "@RG\tID:${sample_id}\tSM:${sample_id}\tPL:${Seq_platform}" ${bwa_args} -K ${bwa_chunk_size} -t $nt ${ref_fasta_dir}/${ref_fasta} ${fastq1} ${fastq2} \
         | sentieon util sort ${bam_option} -i - -r ${ref_fasta_dir}/${ref_fasta} -t $nt -o ${sample_id}.sorted.bam --sam2bam
 
         sentieon driver -r ${ref_fasta_dir}/${ref_fasta} -t $nt -i ${sample_id}.sorted.bam ${qc_driver_args} \