From 4ac7c64dbbdae994f191b3bda1d1609c9dae8082 Mon Sep 17 00:00:00 2001 From: Sergey Koren Date: Mon, 16 Sep 2024 11:05:33 -0400 Subject: [PATCH] Sort after updating node names --- src/Snakefiles/7-combineConsensus.sm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Snakefiles/7-combineConsensus.sm b/src/Snakefiles/7-combineConsensus.sm index 8f29d2b..2fd94ea 100644 --- a/src/Snakefiles/7-combineConsensus.sm +++ b/src/Snakefiles/7-combineConsensus.sm @@ -121,7 +121,7 @@ if [ "{params.haveBAM}" = "True" ]; then echo "" mem_per_core=\`expr {resources.mem_gb} \/ {threads} | awk '{{if (\$1 < 1) print "1G"; else print \$1"G"}}'\` - {params.SAMTOOLS} merge -f -O bam --reference combined.fasta -@{threads} -u - {params.packbam} | {params.SAMTOOLS} sort -m \$mem_per_core -@{threads} | {PYTHON} {VERKKO}/scripts/bam_rename.py ../{input.scfmap} ../{input.tigmap} {params.packcns} > ../{output.bam} 2> sortBAM.err + {params.SAMTOOLS} merge -f -O bam --reference combined.fasta -@{threads} -u - {params.packbam} | {PYTHON} {VERKKO}/scripts/bam_rename.py ../{input.scfmap} ../{input.tigmap} {params.packcns} | {params.SAMTOOLS} sort -m \$mem_per_core -@{threads} -o ../{output.bam} else touch ../{output.bam} fi