From 2fedb5445a35a7d3c56e29e7da28a1fee7d8526f Mon Sep 17 00:00:00 2001
From: Floreal Cabanettes <floreal.cabanettes@inra.fr>
Date: Fri, 24 Aug 2018 18:11:46 +0200
Subject: [PATCH] Fix summary rule
---
snakecnv/mergebatches.snk | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/snakecnv/mergebatches.snk b/snakecnv/mergebatches.snk
index 58f9f8d..be1735e 100644
--- a/snakecnv/mergebatches.snk
+++ b/snakecnv/mergebatches.snk
@@ -179,11 +179,13 @@ rule summary:
input:
expand("filtered/{svtype}/svtyper_{chrom}_{svtype}_genotypes_filtered.vcf.gz", chrom=chromosomes, svtype=variant_types)
params:
- tpl = os.path.join(ROOTPATH, "full.tpl")
+ tpl = os.path.join(ROOTPATH, "full.tpl"),
+ ipynb = os.path.join(ROOTPATH, "Summarized_results.ipynb")
output:
ipynb = "Summarized_results.ipynb",
html = "Summarized_results.html"
threads:
1
shell:
+ "cp {params.ipynb} {output.ipynb}; "
"jupyter nbconvert --to html --template {params.tpl} --execute {output.ipynb}"
\ No newline at end of file
--
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