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Laura Denies
PathoFact
Commits
0adaecb2
Commit
0adaecb2
authored
Apr 23, 2020
by
Valentina Galata
Browse files
adjusted paths to snakemake files (added ext. *.snk) (issue
#18
)
parent
19640026
Changes
5
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Snakefile
View file @
0adaecb2
...
...
@@ -5,7 +5,7 @@ configfile: "config.yaml"
if config["workflow"] == "complete":
include:
"workflows/Combine_PathoFact_workflow"
"workflows/Combine_PathoFact_workflow
.snk
"
rule all:
input:
expand(
...
...
@@ -18,7 +18,7 @@ if config["workflow"] == "complete":
)
elif config["workflow"] == "Tox":
include:
"workflows/Toxin_workflow"
"workflows/Toxin_workflow
.snk
"
rule all:
input:
expand(
...
...
@@ -30,7 +30,7 @@ elif config["workflow"] == "Tox":
)
elif config["workflow"] == "Vir":
include:
"workflows/Virulence_workflow"
"workflows/Virulence_workflow
.snk
"
rule all:
input:
expand(
...
...
@@ -39,7 +39,7 @@ elif config["workflow"] == "Vir":
)
elif config["workflow"] == "AMR":
include:
"workflows/AMR_workflow"
"workflows/AMR_workflow
.snk
"
rule all:
input:
expand(
...
...
workflows/AMR_workflow.snk
View file @
0adaecb2
# include rules for the Analysis part of the workflow
include:
'../rules/Universal/Preprocessing'
'../rules/Universal/Preprocessing
.snk
'
include:
'../rules/Universal/Preprocessing_contig'
'../rules/Universal/Preprocessing_contig
.snk
'
include:
'../rules/AMR/AMR'
'../rules/AMR/AMR
.snk
'
include:
'../rules/AMR/Plasmid'
'../rules/AMR/Plasmid
.snk
'
include:
'../rules/AMR/Phage'
'../rules/AMR/Phage
.snk
'
include:
'../rules/AMR/Combine_MGE_AMR'
'../rules/AMR/Combine_MGE_AMR
.snk
'
# master command
rule AMR_Analysis:
...
...
workflows/Combine_PathoFact_workflow.snk
View file @
0adaecb2
# include rules for the Analysis part of the workflow
include:
'../rules/Universal/Preprocessing'
'../rules/Universal/Preprocessing
.snk
'
include:
'../rules/Universal/SignalP'
'../rules/Universal/SignalP
.snk
'
include:
'../rules/Virulence/Virulence'
'../rules/Virulence/Virulence
.snk
'
include:
'../rules/Virulence/Combine_Virulence_SignalP'
'../rules/Virulence/Combine_Virulence_SignalP
.snk
'
include:
'../rules/Virulence/Virulence_report'
'../rules/Virulence/Virulence_report
.snk
'
include:
'../rules/Toxin/Toxin'
'../rules/Toxin/Toxin
.snk
'
include:
'../rules/Toxin/Combine_Toxin_SignalP'
'../rules/Toxin/Combine_Toxin_SignalP
.snk
'
include:
'../rules/Toxin/Toxin_report'
'../rules/Toxin/Toxin_report
.snk
'
include:
'../rules/Universal/Preprocessing_contig'
'../rules/Universal/Preprocessing_contig
.snk
'
include:
'../rules/AMR/AMR'
'../rules/AMR/AMR
.snk
'
include:
'../rules/AMR/Plasmid'
'../rules/AMR/Plasmid
.snk
'
include:
'../rules/AMR/Phage'
'../rules/AMR/Phage
.snk
'
include:
'../rules/AMR/Combine_MGE_AMR'
'../rules/AMR/Combine_MGE_AMR
.snk
'
include:
'../rules/Universal/Combine_PathoFact'
'../rules/Universal/Combine_PathoFact
.snk
'
# master command
rule Analysis:
...
...
workflows/Toxin_workflow.snk
View file @
0adaecb2
# include rules for the Analysis part of the workflow
include:
'../rules/Universal/Preprocessing'
'../rules/Universal/Preprocessing
.snk
'
include:
'../rules/Universal/SignalP'
'../rules/Universal/SignalP
.snk
'
include:
'../rules/Toxin/Toxin'
'../rules/Toxin/Toxin
.snk
'
include:
'../rules/Toxin/Combine_Toxin_SignalP'
'../rules/Toxin/Combine_Toxin_SignalP
.snk
'
include:
'../rules/Toxin/Toxin_report'
'../rules/Toxin/Toxin_report
.snk
'
# master command
rule Analysis:
...
...
workflows/Virulence_workflow.snk
View file @
0adaecb2
# include rules for the Analysis part of the workflow
include:
'../rules/Universal/Preprocessing'
'../rules/Universal/Preprocessing
.snk
'
include:
'../rules/Universal/SignalP'
'../rules/Universal/SignalP
.snk
'
include:
'../rules/Virulence/Virulence'
'../rules/Virulence/Virulence
.snk
'
include:
'../rules/Virulence/Combine_Virulence_SignalP'
'../rules/Virulence/Combine_Virulence_SignalP
.snk
'
include:
'../rules/Virulence/Virulence_report'
'../rules/Virulence/Virulence_report
.snk
'
# master command
rule Analysis_Virulence:
...
...
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