fix

maxplanck-ie · Nov 15, 2024 · 83a31ce · 83a31ce
1 parent 12f29d0
commit 83a31ce
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git 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
@@ -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