From 8a568b4a632f712dffee59ee03072f041469e396 Mon Sep 17 00:00:00 2001
From: Jeffrey Grover <groverj3@gmail.com>
Date: Tue, 3 Sep 2019 14:24:34 -0700
Subject: [PATCH] Fixed the mosdepth rule so it works now, needed the bam index
 first.

---
 Snakefile   | 1 +
 config.yaml | 3 ++-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/Snakefile b/Snakefile
index 2ff4e79..170f5bd 100644
--- a/Snakefile
+++ b/Snakefile
@@ -285,6 +285,7 @@ rule methyldackel_extract:
 # Get the depth for each sample
 rule mosdepth:
     input:
+        '3_aligned_sorted_markdupes/{sample}.sorted.markdupes.bai',
         bam = '3_aligned_sorted_markdupes/{sample}.sorted.markdupes.bam'
     output:
         '6_mosdepth/{sample}.sorted.markdupes.mosdepth.global.dist.txt',
diff --git a/config.yaml b/config.yaml
index f7c4823..7914f68 100644
--- a/config.yaml
+++ b/config.yaml
@@ -15,7 +15,8 @@ samples:
 
 reference_genome:
     stuff/bwameth_reference/example_ref.fasta
-    # Path to a bwameth indexed genome here with .fasta extension
+    # Path to a reference genome here with .fasta extension
+    # If indexed, then the index will not be regenerated
 
 
 # Options for individual workflow steps