diff --git a/snakePipes/shared/rules/umi_tools.snakefile b/snakePipes/shared/rules/umi_tools.snakefile index c69634fb6..822b0d571 100644 --- a/snakePipes/shared/rules/umi_tools.snakefile +++ b/snakePipes/shared/rules/umi_tools.snakefile @@ -86,7 +86,7 @@ else: elif aligner == "STAR" or aligner == "HISAT2" : rule filter_reads: input: - bamfile = aligner + "/{sample}.bam" + bamfile = "filtered_bam/{sample}.filtered.tmp.bam" output: bamfile = "filtered_bam/{sample}.filtered.bam" shell: """