From de06244bb8e44b409ebff890bfc6517303478da0 Mon Sep 17 00:00:00 2001
From: Anton Kriese <kriese_a@molgen.mpg.de>
Date: Fri, 3 Jun 2022 18:49:10 +0200
Subject: [PATCH] add Illumina to igv batches

---
 workflow/Snakefile | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/workflow/Snakefile b/workflow/Snakefile
index 4ba2308..4660739 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -142,15 +142,14 @@ rule create_igv_batch:
             cat > {output} <<-EOF
 genome {params.path_to_resources}/resources/references/{params.ref_file}
 load {params.path_to_resources}/resources/samples/{wildcards.sample}/{wildcards.ref}/PacBio.bam
+load {params.path_to_resources}/resources/samples/{wildcards.sample}/{wildcards.ref}/Illumina.bam
 goto $REF_REGION
 snapshot {params.path_to_resources}/results/{wildcards.sample}/{wildcards.region}/igv_{wildcards.ref}_screenshot.png
 exit
 EOF
             unset REF_REGION
         """
-        # load "resources/{wildcards.sample}/Illumina.bam"
         # load "results/{wildcards.sample}/{wildcards.region}/MSA"
-        # TODO substitute the all-caps values with actual paths
 
 rule run_igv_batch:
     input: