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Major overhaul of docs #219

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Nov 29, 2018
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Fixed typo
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drpatelh committed Nov 28, 2018
commit 11b776aa8fc720752573149a2859a890c8b78d83
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Expand Up @@ -6,7 +6,7 @@ It is entirely possible to run this pipeline on other clusters, though you will

If you are the only person to be running this pipeline, you can create your config file as `~/.nextflow/config` and it will be applied every time you run Nextflow. Alternatively, save the file anywhere and reference it when running the pipeline with `-c path/to/config` (see the [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html) for more).

A basic configuration comes with the pipeline, which loads the [`conf/base.config`](../../conf/base.config)) by default. This means that you only need to configure the specifics for your system and overwrite any defaults that you want to change.
A basic configuration comes with the pipeline, which loads the [`conf/base.config`](../../conf/base.config) by default. This means that you only need to configure the specifics for your system and overwrite any defaults that you want to change.

## Cluster Environment
By default, pipeline uses the `local` Nextflow executor - in other words, all jobs are run in the login session. If you're using a simple server, this may be fine. If you're using a compute cluster, this is bad as all jobs will run on the head node.
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