@@ -45,11 +45,11 @@ All three input files used by the pipeline for one sample need to be given the s
## Run PathoFact
To run PathoFact the sample name is given in the config.yaml file at "input_file". If wanted more than one sample can be run at the simultanously, for example:
* input_file: ["SAMPLE_A","SAMPLE_B"]
* input_file: ["SAMPLE_A","SAMPLE_B"]
In "OUTDIR" the pathway to the samples are given and the PathoFact results are deposited in the same directory.
* input_file: /path/to/samples
* input_file: /path/to/samples
In "project" an unique name for your project need to be given, for example:
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@@ -57,10 +57,10 @@ In "project" an unique name for your project need to be given, for example:
Lastly in the file called "Snakefile" the required workflow can be selected, which give the following options:
* w = 'complete' (run complete pipeline, default setting)
* w = 'Tox' (run only workflow for Toxin prediction)
* w = 'Vir' (run only workflow for Virulence prediction)
* w = 'AMR' (run only workflow for Antimicrobial resistance and mobile genetic element prediction)
* w = 'complete' (run complete pipeline, default setting)
* w = 'Tox' (run only workflow for Toxin prediction)
* w = 'Vir' (run only workflow for Virulence prediction)
* w = 'AMR' (run only workflow for Antimicrobial resistance and mobile genetic element prediction)
To run the snakemake pipeline and example script is given (run_PathoFact.sh), but the following is the basics to run the pipeline:
