Commit 5cd7ed8f authored by Laura Denies's avatar Laura Denies
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Update README.md

parent 58eef03d
...@@ -45,11 +45,11 @@ All three input files used by the pipeline for one sample need to be given the s ...@@ -45,11 +45,11 @@ All three input files used by the pipeline for one sample need to be given the s
## Run PathoFact ## 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: 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. 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: In "project" an unique name for your project need to be given, for example:
...@@ -57,10 +57,10 @@ In "project" an unique name for your project need to be given, for example: ...@@ -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: 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 = 'complete' (run complete pipeline, default setting)
* w = 'Tox' (run only workflow for Toxin prediction) * w = 'Tox' (run only workflow for Toxin prediction)
* w = 'Vir' (run only workflow for Virulence prediction) * w = 'Vir' (run only workflow for Virulence prediction)
* w = 'AMR' (run only workflow for Antimicrobial resistance and mobile genetic element 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: To run the snakemake pipeline and example script is given (run_PathoFact.sh), but the following is the basics to run the pipeline:
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