From a2da3720bda2e1801443515989f4b40f097f1ae0 Mon Sep 17 00:00:00 2001
From: Floreal Cabanettes <floreal.cabanettes@inra.fr>
Date: Wed, 1 Aug 2018 14:29:23 +0200
Subject: [PATCH] Remove unused genotyping rule
---
snakecnv/tools/genotyping.snk | 22 ----------------------
1 file changed, 22 deletions(-)
diff --git a/snakecnv/tools/genotyping.snk b/snakecnv/tools/genotyping.snk
index 9d55f77..ebe53c8 100644
--- a/snakecnv/tools/genotyping.snk
+++ b/snakecnv/tools/genotyping.snk
@@ -24,25 +24,3 @@ rule svtyping:
shell:
"svtyper_launcher.py -B {input.bamlist} -i {input.sites} -o {output.vcf} -t {threads} "
" 1>{log.stdout} 2>{log.stderr}"
-
-rule genotyping:
- input:
- sites = "{batch}/merge/{chrom}/merge_{chrom}_{svtype}.vcf.gz",
- bamlist = "{batch}/bamlist.list",
- gendermap = "{batch}/genomestrip/gendermap.txt",
- metadatadone = "{batch}/genomestrip/metadata/sample_gender.report.txt",
- genome = REFERENCE
- params:
- metadata = "{batch}/genomestrip/metadata"
- output:
- "{batch}/genotypes/genomestrip_{chrom}_{svtype}_genotypes.vcf.gz"
- threads:
- get_threads("genotyping", 4)
- log:
- stdout = "{batch}/logs/genotyping/{chrom}_genomestrip.o",
- stderr = "{batch}/logs/genotyping/{chrom}_genomestrip.e"
- shell:
- "gstrip_genotyper.sh {input.bamlist} {wildcards.chrom} {input.genome}"
- " {params.metadata} genomestrip/{wildcards.chrom} {input.gendermap} "
- " {input.sites} {output} {threads}"
- " 1>{log.stdout} 2>{log.stderr}"
--
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