From 83d4c2237e12185750320771c246647b8e22609c Mon Sep 17 00:00:00 2001
From: Floreal Cabanettes <floreal.cabanettes@inra.fr>
Date: Wed, 18 Jul 2018 11:49:11 +0200
Subject: [PATCH] Fix simulation workflow
---
snakecnv/popsim.snk | 10 ++++++++++
snakecnv/referencebundle.snk | 2 +-
2 files changed, 11 insertions(+), 1 deletion(-)
diff --git a/snakecnv/popsim.snk b/snakecnv/popsim.snk
index 458325c..310e92b 100644
--- a/snakecnv/popsim.snk
+++ b/snakecnv/popsim.snk
@@ -92,6 +92,16 @@ rule get_fasta_popsim:
if seq.id in CHROMS:
SeqIO.write([seq], f, "fasta")
+rule index_fasta:
+ input:
+ "reference.fasta"
+ output:
+ "reference.fasta.fai"
+ log:
+ "logs/index_fasta.log"
+ shell:
+ "samtools faidx {input} &> {log}"
+
rule buildpop:
input:
**bp_inputs
diff --git a/snakecnv/referencebundle.snk b/snakecnv/referencebundle.snk
index fa15bec..62646c5 100644
--- a/snakecnv/referencebundle.snk
+++ b/snakecnv/referencebundle.snk
@@ -72,7 +72,7 @@ rule index:
log:
"logs/index/{type}.log"
shell:
- "samtools faidx {input} > {log}"
+ "samtools faidx {input} &> {log}"
rule length:
input:
--
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