Merge pull request #431 from jlac/activeDev

fixed gzipped VCF bug in exam and WGS pipelines
CCBR · Oct 16, 2019 · 9b17bda · 9b17bda
2 parents 6dccc34 + a5bdb62
commit 9b17bda
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diff --git a/Rules/admixture_germline.rl b/Rules/admixture_germline.rl
@@ -1,5 +1,5 @@
 rule admixture_germline:
-    input: "exome.strictFilter.vcf.gz"
+    input: "exome.strictFilter.vcf"
     output: vcf=temp("admixture_out/samples_noINDEL_nomissing.recode.vcf"),
             mergedvcf=temp("admixture_out/samples_and_knowns.vcf"),
             ped=temp("admixture_out/samples_and_knowns_filtered.ped"),

diff --git a/Rules/make.germline.network.rl b/Rules/make.germline.network.rl
@@ -1,5 +1,5 @@
 rule make_germline_network:
-    input: "exome.strictFilter.vcf.gz"
+    input: "exome.strictFilter.vcf"
     output: network="sample_network_mqc.png",
     params: rname="make.germline.network"
     shell: """