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Laura Denies
PathoFact
Commits
9d5a1320
Commit
9d5a1320
authored
Apr 21, 2020
by
Valentina Galata
Browse files
rm configfile from all snakemake files except Snakefile (issue
#25
)
parent
c2563441
Changes
16
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Snakefile
View file @
9d5a1320
#Snakefile
# can be overwritten by using --configfile <config file> when calling snakemake
configfile: "config.yaml"
if config["workflow"] == "complete":
include:
"workflows/Combine_PathoFact_workflow"
...
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rules/AMR/AMR.snk
View file @
9d5a1320
...
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@@ -3,7 +3,6 @@
import glob
import os
configfile:"config.yaml"
PROJECT = config["project"]
INPUT = config["input_file"]
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rules/AMR/Combine_MGE_AMR.snk
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9d5a1320
...
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@@ -3,7 +3,6 @@
import glob
import os
configfile:"config.yaml"
PROJECT = config["project"]
INPUT = config["input_file"]
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rules/AMR/Phage.snk
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9d5a1320
...
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@@ -3,7 +3,6 @@
import glob
import os
configfile: "config.yaml"
PROJECT = config["project"]
INPUT = config["input_file"]
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rules/AMR/Plasmid.snk
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9d5a1320
...
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@@ -3,7 +3,6 @@
import glob
import os
configfile: "config.yaml"
PROJECT = config["project"]
INPUT = config["input_file"]
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rules/Toxin/Combine_Toxin_SignalP.snk
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9d5a1320
...
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@@ -3,7 +3,6 @@
import glob
import os
configfile: "config.yaml"
PROJECT = config["project"]
INPUT = config["input_file"]
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rules/Toxin/Toxin.snk
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9d5a1320
...
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@@ -3,7 +3,6 @@
import glob
import os
configfile: "config.yaml"
PROJECT = config["project"]
INPUT = config["input_file"]
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rules/Toxin/Toxin_report.snk
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9d5a1320
...
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@@ -3,7 +3,6 @@
import glob
import os
configfile: "config.yaml"
PROJECT = config["project"]
INPUT = config["input_file"]
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rules/Universal/Combine_PathoFact.snk
View file @
9d5a1320
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@@ -3,7 +3,6 @@
import glob
import os
configfile: "config.yaml"
PROJECT = config["project"]
INPUT = config["input_file"]
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rules/Universal/Preprocessing.snk
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9d5a1320
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@@ -3,7 +3,6 @@
import glob
import os
configfile: "config.yaml"
PROJECT = config["project"]
INPUT = config["input_file"]
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rules/Universal/Preprocessing_contig.snk
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9d5a1320
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@@ -3,7 +3,6 @@
import glob
import os
configfile: "config.yaml"
PROJECT = config["project"]
INPUT = config["input_file"]
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rules/Universal/SignalP.snk
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9d5a1320
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@@ -3,7 +3,6 @@
import glob
import os
configfile: "config.yaml"
PROJECT = config["project"]
INPUT = config["input_file"]
...
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rules/Virulence/Combine_Virulence_SignalP.snk
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9d5a1320
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@@ -3,7 +3,6 @@
import glob
import os
configfile: "config.yaml"
PROJECT = config["project"]
INPUT = config["input_file"]
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rules/Virulence/Virulence.snk
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9d5a1320
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@@ -3,7 +3,6 @@
import glob
import os
configfile: "config.yaml"
PROJECT = config["project"]
INPUT = config["input_file"]
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rules/Virulence/Virulence_report.snk
View file @
9d5a1320
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@@ -3,7 +3,6 @@
import glob
import os
configfile: "config.yaml"
PROJECT = config["project"]
INPUT = config["input_file"]
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workflows/AMR_workflow.snk
View file @
9d5a1320
config: "config.yaml"
# include rules for the Analysis part of the workflow
include:
'../rules/Universal/Preprocessing'
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