From 83a31cefb12893519b7b3b9cf82c864ece39d82a Mon Sep 17 00:00:00 2001
From: "katarzyna.otylia.sikora@gmail.com" <sikora@maximus.ie-freiburg.mpg.de>
Date: Fri, 15 Nov 2024 13:15:19 +0100
Subject: [PATCH] fix

---
 snakePipes/shared/rules/bam_filtering.snakefile | 2 +-
 snakePipes/shared/rules/sambamba.snakefile      | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/snakePipes/shared/rules/bam_filtering.snakefile b/snakePipes/shared/rules/bam_filtering.snakefile
index b6a0616df..960be6e8d 100755
--- a/snakePipes/shared/rules/bam_filtering.snakefile
+++ b/snakePipes/shared/rules/bam_filtering.snakefile
@@ -7,7 +7,7 @@ bam_filter_string = "{} {} {}".format("-F 1024" if dedup else "", "-f 2" if prop
 
 rule samtools_filter:
     input:
-        aligner+"/{sample}.bam"
+        aligner+"/{sample}.markdup.bam"
     output:
         bam = temp("filtered_bam/{sample}.filtered.tmp.bam")
     params:
diff --git a/snakePipes/shared/rules/sambamba.snakefile b/snakePipes/shared/rules/sambamba.snakefile
index 31a92cbc2..8fd4f60b8 100644
--- a/snakePipes/shared/rules/sambamba.snakefile
+++ b/snakePipes/shared/rules/sambamba.snakefile
@@ -7,7 +7,7 @@ rule sambamba_markdup:
        input:
            aligner+"/{sample}.sorted.bam"
        output:
-           aligner+"/{sample}.bam"# duplicate marked
+           aligner+"/{sample}.markdup.bam"# duplicate marked
        threads: lambda wildcards: 10 if 10<max_thread else max_thread
        benchmark: aligner + "/.benchmark/sambamba_markdup.{sample}.benchmark"
        params:
@@ -34,7 +34,7 @@ rule sambamba_flagstat_sorted:
 
 rule sambamba_flagstat:
        input:
-           aligner+"/{sample}.bam"
+           aligner+"/{sample}.markdup.bam"
        output:
            "Sambamba/{sample}.markdup.txt"
        conda: CONDA_SAMBAMBA_ENV
@@ -46,7 +46,7 @@ rule sambamba_flagstat:
 ## index the duplicate marked folder
 rule samtools_index:
     input:
-        aligner+"/{sample}.bam"
+        aligner+"/{sample}.markdup.bam"
     output:
         aligner+"/{sample}.bam.bai"
     conda: CONDA_SHARED_ENV