Commit 9d5a1320 authored by Valentina Galata's avatar Valentina Galata
Browse files

rm configfile from all snakemake files except Snakefile (issue #25)

parent c2563441
#Snakefile #Snakefile
# can be overwritten by using --configfile <config file> when calling snakemake
configfile: "config.yaml"
if config["workflow"] == "complete": if config["workflow"] == "complete":
include: include:
"workflows/Combine_PathoFact_workflow" "workflows/Combine_PathoFact_workflow"
......
...@@ -3,7 +3,6 @@ ...@@ -3,7 +3,6 @@
import glob import glob
import os import os
configfile:"config.yaml"
PROJECT = config["project"] PROJECT = config["project"]
INPUT = config["input_file"] INPUT = config["input_file"]
......
...@@ -3,7 +3,6 @@ ...@@ -3,7 +3,6 @@
import glob import glob
import os import os
configfile:"config.yaml"
PROJECT = config["project"] PROJECT = config["project"]
INPUT = config["input_file"] INPUT = config["input_file"]
......
...@@ -3,7 +3,6 @@ ...@@ -3,7 +3,6 @@
import glob import glob
import os import os
configfile: "config.yaml"
PROJECT = config["project"] PROJECT = config["project"]
INPUT = config["input_file"] INPUT = config["input_file"]
......
...@@ -3,7 +3,6 @@ ...@@ -3,7 +3,6 @@
import glob import glob
import os import os
configfile: "config.yaml"
PROJECT = config["project"] PROJECT = config["project"]
INPUT = config["input_file"] INPUT = config["input_file"]
......
...@@ -3,7 +3,6 @@ ...@@ -3,7 +3,6 @@
import glob import glob
import os import os
configfile: "config.yaml"
PROJECT = config["project"] PROJECT = config["project"]
INPUT = config["input_file"] INPUT = config["input_file"]
......
...@@ -3,7 +3,6 @@ ...@@ -3,7 +3,6 @@
import glob import glob
import os import os
configfile: "config.yaml"
PROJECT = config["project"] PROJECT = config["project"]
INPUT = config["input_file"] INPUT = config["input_file"]
......
...@@ -3,7 +3,6 @@ ...@@ -3,7 +3,6 @@
import glob import glob
import os import os
configfile: "config.yaml"
PROJECT = config["project"] PROJECT = config["project"]
INPUT = config["input_file"] INPUT = config["input_file"]
......
...@@ -3,7 +3,6 @@ ...@@ -3,7 +3,6 @@
import glob import glob
import os import os
configfile: "config.yaml"
PROJECT = config["project"] PROJECT = config["project"]
INPUT = config["input_file"] INPUT = config["input_file"]
......
...@@ -3,7 +3,6 @@ ...@@ -3,7 +3,6 @@
import glob import glob
import os import os
configfile: "config.yaml"
PROJECT = config["project"] PROJECT = config["project"]
INPUT = config["input_file"] INPUT = config["input_file"]
......
...@@ -3,7 +3,6 @@ ...@@ -3,7 +3,6 @@
import glob import glob
import os import os
configfile: "config.yaml"
PROJECT = config["project"] PROJECT = config["project"]
INPUT = config["input_file"] INPUT = config["input_file"]
......
...@@ -3,7 +3,6 @@ ...@@ -3,7 +3,6 @@
import glob import glob
import os import os
configfile: "config.yaml"
PROJECT = config["project"] PROJECT = config["project"]
INPUT = config["input_file"] INPUT = config["input_file"]
......
...@@ -3,7 +3,6 @@ ...@@ -3,7 +3,6 @@
import glob import glob
import os import os
configfile: "config.yaml"
PROJECT = config["project"] PROJECT = config["project"]
INPUT = config["input_file"] INPUT = config["input_file"]
......
...@@ -3,7 +3,6 @@ ...@@ -3,7 +3,6 @@
import glob import glob
import os import os
configfile: "config.yaml"
PROJECT = config["project"] PROJECT = config["project"]
INPUT = config["input_file"] INPUT = config["input_file"]
......
...@@ -3,7 +3,6 @@ ...@@ -3,7 +3,6 @@
import glob import glob
import os import os
configfile: "config.yaml"
PROJECT = config["project"] PROJECT = config["project"]
INPUT = config["input_file"] INPUT = config["input_file"]
......
config: "config.yaml"
# include rules for the Analysis part of the workflow # include rules for the Analysis part of the workflow
include: include:
'../rules/Universal/Preprocessing' '../rules/Universal/Preprocessing'
......
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