diff --git a/workflow/rules/snv.smk b/workflow/rules/snv.smk index 9572cad9..ca00df27 100644 --- a/workflow/rules/snv.smk +++ b/workflow/rules/snv.smk @@ -299,7 +299,8 @@ rule paired_end_read_merger: cohortdir("cohort_consensus.fasta") if config.viloca["consensus"] else reference_file - )+".fai", + ) + + ".fai", output: fname_bam_merged="{dataset}/alignment/REF_aln.merged.bam", fname_sam_merged=temp_with_prefix("{dataset}/alignment/REF_aln.merged.sam"),