Fixed the mosdepth rule so it works now, needed the bam index first.

groverj3 · Sep 3, 2019 · 8a568b4 · 8a568b4
1 parent 5d668d8
commit 8a568b4
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diff --git 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
@@ -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