更新 'tasks/fastqTobam.wdl'

tasks/fastqTobam.wdl

         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
 
+        ls ./
+                  
         sentieon driver -r ${ref_fasta_dir}/${ref_fasta} -t $nt -i ${sample_id}.sorted.bam ${qc_driver_args} \
         --algo MeanQualityByCycle ${sample_id}.mq_metrics.txt \
         --algo QualDistribution ${sample_id}.qd_metrics.txt \
         --algo GCBias --summary ${sample_id}.gc_summary_metrics.txt ${sample_id}.gc_metrics.txt \
         --algo AlignmentStat ${sample_id}.aln_metrics.txt \
         --algo InsertSizeMetricAlgo ${sample_id}.is_metrics.txt
+                  
+        ls ./
 
         sentieon driver -r ${ref_fasta_dir}/${ref_fasta} -t $nt -i ${sample_id}.sorted.bam ${lc_driver_args} \
          --algo LocusCollector \
          ${lc_args} \
          ${sample_id}.score.txt.gz
+                  
+        ls ./
 
         sentieon driver -r ${ref_fasta_dir}/${ref_fasta} -t $nt -i ${sample_id}.sorted.bam ${dedup_driver_args} \
          --algo Dedup \
          --score_info ${sample_id}.score.txt.gz \
          --metrics ${sample_id}.dedup_metrics.txt \
          ${bam_option} ${out_bam} 
+         ls ./
 
     >>>