From d4a439db0e6765de6ba2a167d07d0761d459e578 Mon Sep 17 00:00:00 2001 From: Ryan Routsong Date: Fri, 12 Jan 2024 09:00:07 -0700 Subject: [PATCH] fix: natural name sort bams --- workflow/qc.smk | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflow/qc.smk b/workflow/qc.smk index 824f16e..68a8fb9 100644 --- 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} - """