From c571b4d6492da47217fcefe90fa6f1d618ce641b Mon Sep 17 00:00:00 2001 From: Mathias Johansson Date: Thu, 17 Oct 2024 16:58:59 +0200 Subject: [PATCH] fix umi qc rules --- BALSAMIC/snakemake_rules/umi/qc_umi.rule | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/BALSAMIC/snakemake_rules/umi/qc_umi.rule b/BALSAMIC/snakemake_rules/umi/qc_umi.rule index 3a0e2e06a..cba0e7dcb 100644 --- a/BALSAMIC/snakemake_rules/umi/qc_umi.rule +++ b/BALSAMIC/snakemake_rules/umi/qc_umi.rule @@ -5,7 +5,7 @@ rule picard_umiaware: input: - bam = umi_dir + "{sample_type}.{sample}.consensusfiltered_umi.bam" + bam = umi_dir + "{sample_type}.{sample}_consensusfiltered_umi.bam" output: bam = umi_qc_dir + "{sample_type}.{sample}.picard.umiaware.bam", duplicates = umi_qc_dir + "{sample_type}.{sample}.umi.duplicatemetrics.txt", @@ -36,7 +36,7 @@ UMI_METRICS={output.umimetrics}; rule picard_collecthsmetrics_umi: input: - bam = umi_dir + "{sample_type}.{sample}.consensusfiltered_umi.bam", + bam = umi_dir + "{sample_type}.{sample}_consensusfiltered_umi.bam", bed = config["panel"]["capture_kit"], fa = config["reference"]["reference_genome"], fadict = (config["reference"]["reference_genome"]).replace(".fasta",".dict"), @@ -78,7 +78,7 @@ METRIC_ACCUMULATION_LEVEL=ALL_READS; rule samtools_view_calculatemeanfamilydepth_umi: input: - bam = umi_dir + "{sample_type}.{sample}.consensusfiltered_umi.bam" + bam = umi_dir + "{sample_type}.{sample}_consensusfiltered_umi.bam" output: temp_fl = temp (umi_qc_dir + "{sample_type}.{sample}.umi.temp.fl"), totalsum = umi_qc_dir + "{sample_type}.{sample}.umi.mean_family_depth"