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Laura Denies
PathoFact
Commits
af1f20dc
Commit
af1f20dc
authored
Apr 24, 2020
by
Valentina Galata
Browse files
*.snk to *.smk in files (issue
#18
)
parent
0a7b2929
Changes
5
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Snakefile
View file @
af1f20dc
...
...
@@ -5,7 +5,7 @@ configfile: "config.yaml"
if config["workflow"] == "complete":
include:
"workflows/Combine_PathoFact_workflow.s
n
k"
"workflows/Combine_PathoFact_workflow.s
m
k"
rule all:
input:
expand(
...
...
@@ -18,7 +18,7 @@ if config["workflow"] == "complete":
)
elif config["workflow"] == "Tox":
include:
"workflows/Toxin_workflow.s
n
k"
"workflows/Toxin_workflow.s
m
k"
rule all:
input:
expand(
...
...
@@ -30,7 +30,7 @@ elif config["workflow"] == "Tox":
)
elif config["workflow"] == "Vir":
include:
"workflows/Virulence_workflow.s
n
k"
"workflows/Virulence_workflow.s
m
k"
rule all:
input:
expand(
...
...
@@ -39,7 +39,7 @@ elif config["workflow"] == "Vir":
)
elif config["workflow"] == "AMR":
include:
"workflows/AMR_workflow.s
n
k"
"workflows/AMR_workflow.s
m
k"
rule all:
input:
expand(
...
...
workflows/AMR_workflow.smk
View file @
af1f20dc
# include rules for the Analysis part of the workflow
include:
'../rules/Universal/Preprocessing.s
n
k'
'../rules/Universal/Preprocessing.s
m
k'
include:
'../rules/Universal/Preprocessing_contig.s
n
k'
'../rules/Universal/Preprocessing_contig.s
m
k'
include:
'../rules/AMR/AMR.s
n
k'
'../rules/AMR/AMR.s
m
k'
include:
'../rules/AMR/Plasmid.s
n
k'
'../rules/AMR/Plasmid.s
m
k'
include:
'../rules/AMR/Phage.s
n
k'
'../rules/AMR/Phage.s
m
k'
include:
'../rules/AMR/Combine_MGE_AMR.s
n
k'
'../rules/AMR/Combine_MGE_AMR.s
m
k'
# master command
rule AMR_Analysis:
...
...
workflows/Combine_PathoFact_workflow.smk
View file @
af1f20dc
# include rules for the Analysis part of the workflow
include:
'../rules/Universal/Preprocessing.s
n
k'
'../rules/Universal/Preprocessing.s
m
k'
include:
'../rules/Universal/SignalP.s
n
k'
'../rules/Universal/SignalP.s
m
k'
include:
'../rules/Virulence/Virulence.s
n
k'
'../rules/Virulence/Virulence.s
m
k'
include:
'../rules/Virulence/Combine_Virulence_SignalP.s
n
k'
'../rules/Virulence/Combine_Virulence_SignalP.s
m
k'
include:
'../rules/Virulence/Virulence_report.s
n
k'
'../rules/Virulence/Virulence_report.s
m
k'
include:
'../rules/Toxin/Toxin.s
n
k'
'../rules/Toxin/Toxin.s
m
k'
include:
'../rules/Toxin/Combine_Toxin_SignalP.s
n
k'
'../rules/Toxin/Combine_Toxin_SignalP.s
m
k'
include:
'../rules/Toxin/Toxin_report.s
n
k'
'../rules/Toxin/Toxin_report.s
m
k'
include:
'../rules/Universal/Preprocessing_contig.s
n
k'
'../rules/Universal/Preprocessing_contig.s
m
k'
include:
'../rules/AMR/AMR.s
n
k'
'../rules/AMR/AMR.s
m
k'
include:
'../rules/AMR/Plasmid.s
n
k'
'../rules/AMR/Plasmid.s
m
k'
include:
'../rules/AMR/Phage.s
n
k'
'../rules/AMR/Phage.s
m
k'
include:
'../rules/AMR/Combine_MGE_AMR.s
n
k'
'../rules/AMR/Combine_MGE_AMR.s
m
k'
include:
'../rules/Universal/Combine_PathoFact.s
n
k'
'../rules/Universal/Combine_PathoFact.s
m
k'
# master command
rule Analysis:
...
...
workflows/Toxin_workflow.smk
View file @
af1f20dc
# include rules for the Analysis part of the workflow
include:
'../rules/Universal/Preprocessing.s
n
k'
'../rules/Universal/Preprocessing.s
m
k'
include:
'../rules/Universal/SignalP.s
n
k'
'../rules/Universal/SignalP.s
m
k'
include:
'../rules/Toxin/Toxin.s
n
k'
'../rules/Toxin/Toxin.s
m
k'
include:
'../rules/Toxin/Combine_Toxin_SignalP.s
n
k'
'../rules/Toxin/Combine_Toxin_SignalP.s
m
k'
include:
'../rules/Toxin/Toxin_report.s
n
k'
'../rules/Toxin/Toxin_report.s
m
k'
# master command
rule Analysis:
...
...
workflows/Virulence_workflow.smk
View file @
af1f20dc
# include rules for the Analysis part of the workflow
include:
'../rules/Universal/Preprocessing.s
n
k'
'../rules/Universal/Preprocessing.s
m
k'
include:
'../rules/Universal/SignalP.s
n
k'
'../rules/Universal/SignalP.s
m
k'
include:
'../rules/Virulence/Virulence.s
n
k'
'../rules/Virulence/Virulence.s
m
k'
include:
'../rules/Virulence/Combine_Virulence_SignalP.s
n
k'
'../rules/Virulence/Combine_Virulence_SignalP.s
m
k'
include:
'../rules/Virulence/Virulence_report.s
n
k'
'../rules/Virulence/Virulence_report.s
m
k'
# master command
rule Analysis_Virulence:
...
...
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