From b3b55e090e9242b4bdb2b0e81b4e947c3f1a7474 Mon Sep 17 00:00:00 2001
From: Ticlla Ccenhua Monica Roxana <monicaroxana.ticllaccenhua@unibas.ch>
Date: Wed, 17 Jun 2020 20:57:50 +0200
Subject: [PATCH] correct bug when setting connfiguration with --configfile at
execution, and allow use of environmental variable PWD in config.yaml
---
Snakefile | 13 +++++++++----
config.yaml | 4 ++--
2 files changed, 11 insertions(+), 6 deletions(-)
diff --git a/Snakefile b/Snakefile
index 27daeb2..9fbc4b8 100644
--- a/Snakefile
+++ b/Snakefile
@@ -50,8 +50,9 @@ else:
## Configuration of MetaSnK
##----------------------------------------------------------------------------##
try:
- configfile_path = config['configfile_path']
- print("Configuration file: {}".format(configfile_path), file=sys.stderr)
+ config['RAW_DIR']
+ #configfile_path = config['configfile_path']
+ print("Configuration file provided at execution!", file=sys.stderr)
except:
print("Configuration file config.yaml not especified at execution!", file=sys.stderr)
try:
@@ -66,12 +67,16 @@ except:
configfile_path = workflow_path + "/config.yaml"
configfile: configfile_path
print("... Configuration file: {}".format(configfile_path), file=sys.stderr)
+finally:
+ print("Configuration of MetaSnk:", file=sys.stderr)
+ my_temp=[print(" {}:{}\n".format(key,value), file=sys.stderr) for key,value in config.items()]
##----------------------------------------------------------------------------##
## Define paths and local variables
##----------------------------------------------------------------------------##
-RAW_FASTQ_DIR = config['RAW_DIR']
-OUT_DIR = config['OUT_DIR']
+PWD = os.environ["PWD"]
+RAW_FASTQ_DIR = eval(config['RAW_DIR'])
+OUT_DIR = eval(config['OUT_DIR'])
METASNK_DB_DIR = os.environ["METASNK_DBS"]
SHUB_PREQC_SIF = 'shub://mticlla/MetagenomicSnake:preqc_v0_1'
SHUB_METAPROF_SIF = 'shub://mticlla/OmicSingularities:metaprof'
diff --git a/config.yaml b/config.yaml
index 6104a18..5a2d55c 100644
--- a/config.yaml
+++ b/config.yaml
@@ -11,9 +11,9 @@
#
# Absolute PATH to folder where to find fastq files
-RAW_DIR: '/home/mticlla/Documents/Git_repositories/metagenomicsnake_testdata/data/raw'
+RAW_DIR: "PWD+'/data/raw'"
# Absolute PATH to folder where to place output files
-OUT_DIR: '/home/mticlla/Documents/Git_repositories/metagenomicsnake_testdata/data/interim/MetaSnk'
+OUT_DIR: "PWD+'/data/interim/MetaSnk'"
#
SAMPLE_UNITS:
--
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