From 3bd38e97d04e842bdee08872e8e2980706d0fe71 Mon Sep 17 00:00:00 2001 From: Bernt Popp Date: Thu, 31 Aug 2023 07:14:59 +0200 Subject: [PATCH] fix error --- analyses/alignment/bqsr_bams.smk | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/analyses/alignment/bqsr_bams.smk b/analyses/alignment/bqsr_bams.smk index 84e7a0d..4167d4e 100644 --- a/analyses/alignment/bqsr_bams.smk +++ b/analyses/alignment/bqsr_bams.smk @@ -87,7 +87,7 @@ rule apply_bqsr: shell: """ # Use GATK's ApplyBQSRS to apply base recalibration - gatk --java-options '-Xms4000m -Xmx7g -Djava.io.tmpdir={resources.tmpdir} -Dsamjdk.compression_level=6' ApplyBQSRS \ + gatk --java-options '-Xms4000m -Xmx7g -Djava.io.tmpdir={resources.tmpdir} -Dsamjdk.compression_level=6' ApplyBQSR \ -I "{input.bam_file}" \ -bqsr "{input.recal_table}" \ -O "{output.bqsr_bam}" 2> {log.apply_bqsr}