Commit 25774a3f authored by Valentina Galata's avatar Valentina Galata
Browse files

format fix in workflow files (issue #26)

parent 086684df
config: "config.yaml"
# include rules for the Analysis part of the workflow
include:
'../rules/Universal/Preprocessing'
'../rules/Universal/Preprocessing'
include:
'../rules/Universal/Preprocessing_contig'
'../rules/Universal/Preprocessing_contig'
include:
'../rules/AMR/AMR'
'../rules/AMR/AMR'
include:
'../rules/AMR/Plasmid'
'../rules/AMR/Plasmid'
include:
'../rules/AMR/Phage'
'../rules/AMR/Phage'
include:
'../rules/AMR/Combine_MGE_AMR'
'../rules/AMR/Combine_MGE_AMR'
# master command
rule AMR_Analysis:
input:
expand(["{OUTDIR}/{project}/MGE/phage/{input_file}_VIRSorter_aggregated.csv",
"{OUTDIR}/{project}/MGE/phage/{input_file}_VirFinder_aggregated.csv",
"{OUTDIR}/{project}/MGE/plasmid/{input_file}_plasflow_prediction_final.tsv",
"{OUTDIR}/{project}/AMR_MGE_prediction_{input_file}_report.tsv",
"{OUTDIR}/{project}/AMR/{input_file}_AMR_MGE_prediction_detailed.tsv"]
, OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"])
output:
touch('AMR_analyis.done')
input:
expand(
[
"{OUTDIR}/{project}/MGE/phage/{input_file}_VIRSorter_aggregated.csv",
"{OUTDIR}/{project}/MGE/phage/{input_file}_VirFinder_aggregated.csv",
"{OUTDIR}/{project}/MGE/plasmid/{input_file}_plasflow_prediction_final.tsv",
"{OUTDIR}/{project}/AMR_MGE_prediction_{input_file}_report.tsv",
"{OUTDIR}/{project}/AMR/{input_file}_AMR_MGE_prediction_detailed.tsv"
],
OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
)
output:
touch('AMR_analyis.done')
# include rules for the Analysis part of the workflow
include:
'../rules/Universal/Preprocessing'
'../rules/Universal/Preprocessing'
include:
'../rules/Universal/SignalP'
'../rules/Universal/SignalP'
include:
'../rules/Virulence/Virulence'
'../rules/Virulence/Virulence'
include:
'../rules/Virulence/Combine_Virulence_SignalP'
'../rules/Virulence/Combine_Virulence_SignalP'
include:
'../rules/Virulence/Virulence_report'
'../rules/Virulence/Virulence_report'
include:
'../rules/Toxin/Toxin'
'../rules/Toxin/Toxin'
include:
'../rules/Toxin/Combine_Toxin_SignalP'
'../rules/Toxin/Combine_Toxin_SignalP'
include:
'../rules/Toxin/Toxin_report'
'../rules/Toxin/Toxin_report'
include:
'../rules/Universal/Preprocessing_contig'
'../rules/Universal/Preprocessing_contig'
include:
'../rules/AMR/AMR'
'../rules/AMR/AMR'
include:
'../rules/AMR/Plasmid'
'../rules/AMR/Plasmid'
include:
'../rules/AMR/Phage'
'../rules/AMR/Phage'
include:
'../rules/AMR/Combine_MGE_AMR'
'../rules/AMR/Combine_MGE_AMR'
include:
'../rules/Universal/Combine_PathoFact'
'../rules/Universal/Combine_PathoFact'
# master command
rule Analysis:
input:
expand(["{OUTDIR}/{project}/AMR/{input_file}_AMR_MGE_prediction_detailed.tsv",
"{OUTDIR}/{project}/Toxin_gene_library_{input_file}_report.tsv",
"{OUTDIR}/{project}/PathoFact_{input_file}_predictions.csv"],
OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"])
output:
touch('PathoFact_analyis.done')
input:
expand(
[
"{OUTDIR}/{project}/AMR/{input_file}_AMR_MGE_prediction_detailed.tsv",
"{OUTDIR}/{project}/Toxin_gene_library_{input_file}_report.tsv",
"{OUTDIR}/{project}/PathoFact_{input_file}_predictions.csv"
],
OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
)
output:
touch('PathoFact_analyis.done')
# include rules for the Analysis part of the workflow
include:
'../rules/Universal/Preprocessing'
'../rules/Universal/Preprocessing'
include:
'../rules/Universal/SignalP'
'../rules/Universal/SignalP'
include:
'../rules/Toxin/Toxin'
'../rules/Toxin/Toxin'
include:
'../rules/Toxin/Combine_Toxin_SignalP'
'../rules/Toxin/Combine_Toxin_SignalP'
include:
'../rules/Toxin/Toxin_report'
'../rules/Toxin/Toxin_report'
# master command
rule Analysis:
input:
expand(["{OUTDIR}/{project}/SignalP/aggregated/{input_file}_SignalP_results.txt",
"{OUTDIR}/{project}/Toxin_gene_library_{input_file}_report.tsv",
"{OUTDIR}/{project}/Toxin_prediction_{input_file}_report.csv"], OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"])
output:
touch('Toxin_analyis.done')
input:
expand(
[
"{OUTDIR}/{project}/SignalP/aggregated/{input_file}_SignalP_results.txt",
"{OUTDIR}/{project}/Toxin_gene_library_{input_file}_report.tsv",
"{OUTDIR}/{project}/Toxin_prediction_{input_file}_report.csv"
],
OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
)
output:
touch('Toxin_analyis.done')
# include rules for the Analysis part of the workflow
include:
'../rules/Universal/Preprocessing'
'../rules/Universal/Preprocessing'
include:
'../rules/Universal/SignalP'
'../rules/Universal/SignalP'
include:
'../rules/Virulence/Virulence'
'../rules/Virulence/Virulence'
include:
'../rules/Virulence/Combine_Virulence_SignalP'
'../rules/Virulence/Combine_Virulence_SignalP'
include:
'../rules/Virulence/Virulence_report'
'../rules/Virulence/Virulence_report'
# master command
rule Analysis_Virulence:
input:
expand(["{OUTDIR}/{project}/SignalP/aggregated/{input_file}_SignalP_results.txt",
"{OUTDIR}/{project}/Virulence_prediction_{input_file}_report.csv"],
OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"])
output:
touch('virulence_analyis.done')
input:
expand(
[
"{OUTDIR}/{project}/SignalP/aggregated/{input_file}_SignalP_results.txt",
"{OUTDIR}/{project}/Virulence_prediction_{input_file}_report.csv"
],
OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
)
output:
touch('virulence_analyis.done')
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