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Merge branch 'master' of github.com:aryam7/varCA
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aryarm committed Jun 27, 2020
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Expand Up @@ -43,7 +43,7 @@ conda install -c bioconda -c conda-forge 'snakemake==5.18.0'
qsub run.bash
```

The pipeline is written as Snakefiles, so it must be executed via [Snakemake](https://snakemake.readthedocs.io). See the [`run.bash` script](run.bash) for an example. Make sure to provide required input and options in the [config files](configs) before executing. The config files are currently configured to run the pipeline on the example data provided.
The pipeline is written as a Snakefile, so it must be executed via [Snakemake](https://snakemake.readthedocs.io). See the [`run.bash` script](run.bash) for an example. Make sure to provide required input and options in the [config files](configs) before executing. The config files are currently configured to run the pipeline on the example data provided.

### If this is your first time using Snakemake
We highly recommend that you run `snakemake --help` to learn about all of the options available to you. You might discover, for example, that calling Snakemake with the `-n -p -r` flags can be a helpful way to check that the pipeline will be executed correctly before you run it. This can also be a good way to familiarize yourself with the steps of the pipeline and their inputs and outputs (the latter of which are inputs to the first rule in each workflow -- ie the `all` rule).
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