Commit af1f20dc authored by Valentina Galata's avatar Valentina Galata
Browse files

*.snk to *.smk in files (issue #18)

parent 0a7b2929
......@@ -5,7 +5,7 @@ configfile: "config.yaml"
if config["workflow"] == "complete":
include:
"workflows/Combine_PathoFact_workflow.snk"
"workflows/Combine_PathoFact_workflow.smk"
rule all:
input:
expand(
......@@ -18,7 +18,7 @@ if config["workflow"] == "complete":
)
elif config["workflow"] == "Tox":
include:
"workflows/Toxin_workflow.snk"
"workflows/Toxin_workflow.smk"
rule all:
input:
expand(
......@@ -30,7 +30,7 @@ elif config["workflow"] == "Tox":
)
elif config["workflow"] == "Vir":
include:
"workflows/Virulence_workflow.snk"
"workflows/Virulence_workflow.smk"
rule all:
input:
expand(
......@@ -39,7 +39,7 @@ elif config["workflow"] == "Vir":
)
elif config["workflow"] == "AMR":
include:
"workflows/AMR_workflow.snk"
"workflows/AMR_workflow.smk"
rule all:
input:
expand(
......
# include rules for the Analysis part of the workflow
include:
'../rules/Universal/Preprocessing.snk'
'../rules/Universal/Preprocessing.smk'
include:
'../rules/Universal/Preprocessing_contig.snk'
'../rules/Universal/Preprocessing_contig.smk'
include:
'../rules/AMR/AMR.snk'
'../rules/AMR/AMR.smk'
include:
'../rules/AMR/Plasmid.snk'
'../rules/AMR/Plasmid.smk'
include:
'../rules/AMR/Phage.snk'
'../rules/AMR/Phage.smk'
include:
'../rules/AMR/Combine_MGE_AMR.snk'
'../rules/AMR/Combine_MGE_AMR.smk'
# master command
rule AMR_Analysis:
......
# include rules for the Analysis part of the workflow
include:
'../rules/Universal/Preprocessing.snk'
'../rules/Universal/Preprocessing.smk'
include:
'../rules/Universal/SignalP.snk'
'../rules/Universal/SignalP.smk'
include:
'../rules/Virulence/Virulence.snk'
'../rules/Virulence/Virulence.smk'
include:
'../rules/Virulence/Combine_Virulence_SignalP.snk'
'../rules/Virulence/Combine_Virulence_SignalP.smk'
include:
'../rules/Virulence/Virulence_report.snk'
'../rules/Virulence/Virulence_report.smk'
include:
'../rules/Toxin/Toxin.snk'
'../rules/Toxin/Toxin.smk'
include:
'../rules/Toxin/Combine_Toxin_SignalP.snk'
'../rules/Toxin/Combine_Toxin_SignalP.smk'
include:
'../rules/Toxin/Toxin_report.snk'
'../rules/Toxin/Toxin_report.smk'
include:
'../rules/Universal/Preprocessing_contig.snk'
'../rules/Universal/Preprocessing_contig.smk'
include:
'../rules/AMR/AMR.snk'
'../rules/AMR/AMR.smk'
include:
'../rules/AMR/Plasmid.snk'
'../rules/AMR/Plasmid.smk'
include:
'../rules/AMR/Phage.snk'
'../rules/AMR/Phage.smk'
include:
'../rules/AMR/Combine_MGE_AMR.snk'
'../rules/AMR/Combine_MGE_AMR.smk'
include:
'../rules/Universal/Combine_PathoFact.snk'
'../rules/Universal/Combine_PathoFact.smk'
# master command
rule Analysis:
......
# include rules for the Analysis part of the workflow
include:
'../rules/Universal/Preprocessing.snk'
'../rules/Universal/Preprocessing.smk'
include:
'../rules/Universal/SignalP.snk'
'../rules/Universal/SignalP.smk'
include:
'../rules/Toxin/Toxin.snk'
'../rules/Toxin/Toxin.smk'
include:
'../rules/Toxin/Combine_Toxin_SignalP.snk'
'../rules/Toxin/Combine_Toxin_SignalP.smk'
include:
'../rules/Toxin/Toxin_report.snk'
'../rules/Toxin/Toxin_report.smk'
# master command
rule Analysis:
......
# include rules for the Analysis part of the workflow
include:
'../rules/Universal/Preprocessing.snk'
'../rules/Universal/Preprocessing.smk'
include:
'../rules/Universal/SignalP.snk'
'../rules/Universal/SignalP.smk'
include:
'../rules/Virulence/Virulence.snk'
'../rules/Virulence/Virulence.smk'
include:
'../rules/Virulence/Combine_Virulence_SignalP.snk'
'../rules/Virulence/Combine_Virulence_SignalP.smk'
include:
'../rules/Virulence/Virulence_report.snk'
'../rules/Virulence/Virulence_report.smk'
# master command
rule Analysis_Virulence:
......
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