From baafabac4e1746bf8766719bb115df0c8d9d2cba Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Fri, 9 Feb 2024 15:01:40 +0100
Subject: [PATCH] Update Snakefile
Removed og file creation
---
Snakefile | 3 ---
1 file changed, 3 deletions(-)
diff --git a/Snakefile b/Snakefile
index c0e1e7b..0ec2a67 100644
--- a/Snakefile
+++ b/Snakefile
@@ -78,7 +78,6 @@ rule pggb_on_chr:
gzi="data/chrInputs/{chromosome}.fa.gz.gzi"
output:
gfa="data/chrGraphs/{chromosome}.gfa"
- og="data/chrGraphs/{chromosome}.gfa"
threads: 16
params:
pggb=config['pggb.params'],
@@ -94,8 +93,6 @@ rule pggb_on_chr:
tee {log.cmd}
echo $(ls data/chrGraphs/{wildcards.chromosome})
mv data/chrGraphs/{wildcards.chromosome}/*.gfa {output.gfa}
- apptainer run --app odgi {params.apppath}/PanGeTools.sif \
- build -s -O -t {threads} -P -g {output.gfa} -o {output.og}
"""
def availGraphs(wildcards):
--
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