add Illumina to igv batches

kriese · Jun 3, 2022 · de06244 · de06244
1 parent 371d209
commit de06244
Showing 1 changed file with 1 addition and 2 deletions.
diff --git 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: