Merge pull request #13 from sunbeam-labs/12-num_reads-and-sliding_cov…

…erage-should-use-filtered-input Update targets to all filtered
sunbeam-labs · Nov 2, 2023 · 5509996 · 5509996
2 parents 9a0ea8c + ba2fe5a
commit 5509996
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/sbx_mapping.smk b/sbx_mapping.smk
@@ -160,7 +160,7 @@ rule samtools_index:
 
 rule get_sliding_coverage:
     input:
-        MAPPING_FP / "{genome}" / "{sample}.bam",
+        MAPPING_FP / "filtered" / "{genome}" / "{sample}.bam",
     output:
         MAPPING_FP / "intermediates" / "{genome}" / "{sample}_sliding_coverage.csv",
     params:
@@ -231,7 +231,7 @@ rule samtools_summarize_filtered_coverage:
 
 rule summarize_num_mapped_reads:
     input:
-        MAPPING_FP / "{genome}" / "{sample}.bam",
+        MAPPING_FP / "filtered" / "{genome}" / "{sample}.bam",
     output:
         MAPPING_FP / "intermediates" / "{genome}" / "{sample}_numReads.csv",
     conda: