fix: sample has umis (#265)

Co-authored-by: Felix Mölder <[email protected]>
snakemake-workflows · Aug 25, 2023 · 914ddfa · 914ddfa
1 parent cc486d7
commit 914ddfa
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
@@ -392,9 +392,9 @@ def get_markduplicates_extra(wc):
     c = config["params"]["picard"]["MarkDuplicates"]
 
     if sample_has_umis(wc.sample):
-        b = ""
-    else:
         b = "--BARCODE_TAG RX"
+    else:
+        b = ""
 
     if is_activated("calc_consensus_reads"):
         d = "--TAG_DUPLICATE_SET_MEMBERS true"
@@ -898,7 +898,7 @@ def get_umi_fastq(wildcards):
 
 
 def sample_has_umis(sample):
-    return pd.isna(samples.loc[sample, "umi_read"])
+    return pd.notna(samples.loc[sample, "umi_read"])
 
 
 def get_umi_read_structure(wildcards):

diff --git a/workflow/rules/mapping.smk b/workflow/rules/mapping.smk
@@ -46,9 +46,9 @@ rule annotate_umis:
 
 rule mark_duplicates:
     input:
-        bams=lambda wc: "results/mapped/{sample}.bam"
+        bams=lambda wc: "results/mapped/{sample}.annotated.bam"
         if sample_has_umis(wc.sample)
-        else "results/mapped/{sample}.annotated.bam",
+        else "results/mapped/{sample}.bam",
     output:
         bam=temp("results/dedup/{sample}.bam"),
         metrics="results/qc/dedup/{sample}.metrics.txt",