From 09583c2a7fe6d07bb5d9c15d4232a7db1482cd4d Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Mon, 26 Feb 2018 15:58:59 +0100
Subject: [PATCH] use srcdir in stead of repeated joins
---
Snakefile | 21 ++++++++++-----------
1 file changed, 10 insertions(+), 11 deletions(-)
diff --git a/Snakefile b/Snakefile
index 82566ee..f6b91ae 100644
--- a/Snakefile
+++ b/Snakefile
@@ -17,20 +17,19 @@ FEMALE_THRESHOLD = config.get("FEMALE_THRESHOLD", 0.6)
FASTQ_COUNT = config.get("FASTQ_COUNT")
MAX_BASES = config.get("MAX_BASES", "")
-_this_dir = workflow.current_basedir
+def fsrc_dir(*args):
+ """Wrapper around snakemake's srcdir to work like os.path.join"""
+ if len(args) == 1:
+ return srcdir(args[0])
+ return srcdir(join(*args))
-
-env_dir = join(_this_dir, "envs")
-main_env = join(_this_dir, "environment.yml")
-
-settings_template = join(join(_this_dir, "templates"), "pipeline_settings.md.j2")
-covpy = join(join(_this_dir, "src"), "covstats.py")
-colpy = join(join(_this_dir, "src"), "collect_stats.py")
-vs_py = join(join(_this_dir, "src"), "vcfstats.py")
-mpy = join(join(_this_dir, "src"), "merge_stats.py")
+covpy = fsrc_dir("src", "covstats.py")
+colpy = fsrc_dir("src", "collect_stats.py")
+vs_py = fsrc_dir("src", "vcfstats.py")
+mpy = fsrc_dir("src", "merge_stats.py")
if FASTQ_COUNT is None:
- fqc = "python {0}".format(join(join(_this_dir, "src"), "fastq-count.py"))
+ fqc = "python {0}".format(fsrc_dir("src", "fastq-count.py"))
else:
fqc = FASTQ_COUNT
--
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