diff --git a/Snakemake/IMAGE_vqsr/rules/intersect_vcf.smk b/Snakemake/IMAGE_vqsr/rules/intersect_vcf.smk index cec0217db0c2dc69dc50d45cdedf4b38a842503f..de8717fd13627660b2447090fa19ae7b499a1b4c 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"],