fix: natural name sort bams

OpenOmics · Jan 12, 2024 · d4a439d · d4a439d
1 parent 340fc9a
commit d4a439d
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/workflow/qc.smk b/workflow/qc.smk
@@ -69,8 +69,8 @@ rule bwa:
     log: config['out_to'] + "/logs/" + config["project"] + "/bwa_mem/{sids}.log"
     shell:
         """
-        bwa mem -t {threads} {params.host_genome} {input.in_read1} {input.in_read2} | samtools sort -@ {threads} -o {output.aligntoA} -
-        bwa mem -t {threads} {params.path_genome} {input.in_read1} {input.in_read2} | samtools sort -@ {threads} -o {output.aligntoB} -
+        bwa mem -t {threads} {params.host_genome} {input.in_read1} {input.in_read2} | samtools sort -@ {threads} -n -o {output.aligntoA} -
+        bwa mem -t {threads} {params.path_genome} {input.in_read1} {input.in_read2} | samtools sort -@ {threads} -n -o {output.aligntoB} -
         """