From ba2fe5ac0c40afef2e73ed158542bfcbe3afbdc9 Mon Sep 17 00:00:00 2001
From: ctbus <ctbushman@gmail.com>
Date: Thu, 2 Nov 2023 15:57:27 -0400
Subject: [PATCH] Update targets to all filtered

---
 sbx_mapping.smk | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sbx_mapping.smk b/sbx_mapping.smk
index 8f436bb..d59a5ba 100644
--- 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: