diff --git a/workflow/rules/bwa_mem.smk b/workflow/rules/bwa_mem.smk index f5e53aa..5b81e88 100644 --- a/workflow/rules/bwa_mem.smk +++ b/workflow/rules/bwa_mem.smk @@ -18,6 +18,6 @@ rule bwa_mem: shell: """ mkdir -p results/arima_mapping_pipeline/RAW_DIR - bwa mem -M -t {config[arima][CPU]} {input.REF} {input.forward_hic} | samtools view -@ {config[arima][CPU]} -Sb - > {output.bam1} >> {log} 2>&1 - bwa mem -M -t {config[arima][CPU]} {input.REF} {input.reverse_hic} | samtools view -@ {config[arima][CPU]} -Sb - > {output.bam2} >> {log} 2>&1 + bwa mem -M -t {config[arima][CPU]} {input.REF} {input.forward_hic} | samtools view -@ {config[arima][CPU]} -Sb - > {output.bam1} + bwa mem -M -t {config[arima][CPU]} {input.REF} {input.reverse_hic} | samtools view -@ {config[arima][CPU]} -Sb - > {output.bam2} """ \ No newline at end of file