Commit 0adaecb2 authored by Valentina Galata's avatar Valentina Galata
Browse files

adjusted paths to snakemake files (added ext. *.snk) (issue #18)

parent 19640026
...@@ -5,7 +5,7 @@ configfile: "config.yaml" ...@@ -5,7 +5,7 @@ configfile: "config.yaml"
if config["workflow"] == "complete": if config["workflow"] == "complete":
include: include:
"workflows/Combine_PathoFact_workflow" "workflows/Combine_PathoFact_workflow.snk"
rule all: rule all:
input: input:
expand( expand(
...@@ -18,7 +18,7 @@ if config["workflow"] == "complete": ...@@ -18,7 +18,7 @@ if config["workflow"] == "complete":
) )
elif config["workflow"] == "Tox": elif config["workflow"] == "Tox":
include: include:
"workflows/Toxin_workflow" "workflows/Toxin_workflow.snk"
rule all: rule all:
input: input:
expand( expand(
...@@ -30,7 +30,7 @@ elif config["workflow"] == "Tox": ...@@ -30,7 +30,7 @@ elif config["workflow"] == "Tox":
) )
elif config["workflow"] == "Vir": elif config["workflow"] == "Vir":
include: include:
"workflows/Virulence_workflow" "workflows/Virulence_workflow.snk"
rule all: rule all:
input: input:
expand( expand(
...@@ -39,7 +39,7 @@ elif config["workflow"] == "Vir": ...@@ -39,7 +39,7 @@ elif config["workflow"] == "Vir":
) )
elif config["workflow"] == "AMR": elif config["workflow"] == "AMR":
include: include:
"workflows/AMR_workflow" "workflows/AMR_workflow.snk"
rule all: rule all:
input: input:
expand( expand(
......
# 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.snk'
include: include:
'../rules/Universal/Preprocessing_contig' '../rules/Universal/Preprocessing_contig.snk'
include: include:
'../rules/AMR/AMR' '../rules/AMR/AMR.snk'
include: include:
'../rules/AMR/Plasmid' '../rules/AMR/Plasmid.snk'
include: include:
'../rules/AMR/Phage' '../rules/AMR/Phage.snk'
include: include:
'../rules/AMR/Combine_MGE_AMR' '../rules/AMR/Combine_MGE_AMR.snk'
# master command # master command
rule AMR_Analysis: rule AMR_Analysis:
......
# 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.snk'
include: include:
'../rules/Universal/SignalP' '../rules/Universal/SignalP.snk'
include: include:
'../rules/Virulence/Virulence' '../rules/Virulence/Virulence.snk'
include: include:
'../rules/Virulence/Combine_Virulence_SignalP' '../rules/Virulence/Combine_Virulence_SignalP.snk'
include: include:
'../rules/Virulence/Virulence_report' '../rules/Virulence/Virulence_report.snk'
include: include:
'../rules/Toxin/Toxin' '../rules/Toxin/Toxin.snk'
include: include:
'../rules/Toxin/Combine_Toxin_SignalP' '../rules/Toxin/Combine_Toxin_SignalP.snk'
include: include:
'../rules/Toxin/Toxin_report' '../rules/Toxin/Toxin_report.snk'
include: include:
'../rules/Universal/Preprocessing_contig' '../rules/Universal/Preprocessing_contig.snk'
include: include:
'../rules/AMR/AMR' '../rules/AMR/AMR.snk'
include: include:
'../rules/AMR/Plasmid' '../rules/AMR/Plasmid.snk'
include: include:
'../rules/AMR/Phage' '../rules/AMR/Phage.snk'
include: include:
'../rules/AMR/Combine_MGE_AMR' '../rules/AMR/Combine_MGE_AMR.snk'
include: include:
'../rules/Universal/Combine_PathoFact' '../rules/Universal/Combine_PathoFact.snk'
# master command # master command
rule Analysis: rule Analysis:
......
# 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.snk'
include: include:
'../rules/Universal/SignalP' '../rules/Universal/SignalP.snk'
include: include:
'../rules/Toxin/Toxin' '../rules/Toxin/Toxin.snk'
include: include:
'../rules/Toxin/Combine_Toxin_SignalP' '../rules/Toxin/Combine_Toxin_SignalP.snk'
include: include:
'../rules/Toxin/Toxin_report' '../rules/Toxin/Toxin_report.snk'
# master command # master command
rule Analysis: rule Analysis:
......
# 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.snk'
include: include:
'../rules/Universal/SignalP' '../rules/Universal/SignalP.snk'
include: include:
'../rules/Virulence/Virulence' '../rules/Virulence/Virulence.snk'
include: include:
'../rules/Virulence/Combine_Virulence_SignalP' '../rules/Virulence/Combine_Virulence_SignalP.snk'
include: include:
'../rules/Virulence/Virulence_report' '../rules/Virulence/Virulence_report.snk'
# master command # master command
rule Analysis_Virulence: rule Analysis_Virulence:
......
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