From 8e71a4813093b6d99392e01c8e742f5fe986d1be Mon Sep 17 00:00:00 2001
From: mariabernard <maria.bernard@jouy.inra.fr>
Date: Mon, 1 Apr 2019 10:46:54 +0200
Subject: [PATCH] IMAGE_vqsr: rename intersect rules
---
Snakemake/IMAGE_vqsr/rules/intersect_vcf.smk | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/Snakemake/IMAGE_vqsr/rules/intersect_vcf.smk b/Snakemake/IMAGE_vqsr/rules/intersect_vcf.smk
index cec0217..de8717f 100644
--- a/Snakemake/IMAGE_vqsr/rules/intersect_vcf.smk
+++ b/Snakemake/IMAGE_vqsr/rules/intersect_vcf.smk
@@ -18,7 +18,7 @@ def get_ordered_input_uniq(wildcards):
return input
-rule uniq :
+rule uniq_variants :
input :
get_ordered_input_uniq
output :
@@ -32,7 +32,7 @@ rule uniq :
{config[bin][bgzip]} -c {output.vcf} > {output.gzip}
"""
-rule concat_uniq:
+rule concat_uniq_variants:
input :
expand("results/intersect/uniq_{caller}_variants.vcf.gz.tbi", caller=["freebayes","mpileup","gatk"]),
vcfs=expand("results/intersect/uniq_{caller}_variants.vcf.gz", caller=["freebayes","mpileup","gatk"]),
@@ -47,7 +47,7 @@ rule concat_uniq:
{config[bin][bcftools]} concat -a {input.vcfs} | {config[bin][bcftools]} sort - -m {params.mem} -o {output} -O z
"""
-rule common_variant:
+rule common_variants:
input:
config["GATK_variants"],
config["Freebayes_variants"],
--
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