Merge pull request #2 from bentsherman/patch-1

Update docs.md

docs.md

@@ -2,62 +2,66 @@
 
 ## Pre-requisites
 
-Make sure to have configured the XPACK license and the plugin as described 
-in the [README](README.md#configuration) document. 
+Make sure to configure the XPACK license and the plugin as described
+in the [README](README.md#configuration).
 
-## AWS Batch pro executor 
+## AWS Batch Pro executor
 
-The `xpack-amzn` plugin implements an advanced version of AWS Batch executor 
-for Nextflow that allows using a shared file system in place of AWS S3 bucket 
-as the pipeline work directory to ingest pipeline data. 
+The `xpack-amzn` plugin implements an advanced version of the AWS Batch executor
+for Nextflow, which supports the use of a shared file system instead of an S3 bucket
+as the pipeline work directory.
 
-## Use of AWS EFS file system with Nextflow 
+## Using Amazon EFS
 
-AWS [EFS](https://aws.amazon.com/efs/) is a shared file-system based on the 
+[Amazon EFS](https://aws.amazon.com/efs/) is a shared file-system based on the 
 NFS protocol provided by AWS. 
 
-To learn about EFS details and how to create EFS instance check the AWS documentation
-at [this link](https://docs.aws.amazon.com/efs/latest/ug/creating-using-create-fs.html).
+To learn more about EFS and how to create an EFS instance, check out the [AWS documentation](https://docs.aws.amazon.com/efs/latest/ug/creating-using-create-fs.html).
 
-Once you have created one or more file systems, to make accessible in your 
-pipeline execution add the `efsVolumes` declaration in your configuration 
-file as shown below:
+Once you have created your desired EFS instances, you can make them accessible to your
+pipeline with the `efsVolumes` option in your Nextflow configuration:
 
+```groovy
+aws.batch.efsVolumes.'efs-1234567890'.mountPath = '/mnt/efs'
 ```
-aws.batch.efsVolumes.'efs-1234567890'.mountPath = '/mnt/fsx'
+
+In the above snippet, replace `efs-1234567890` with the ID of your EFS instance and
+the path `/mnt/efs` with one of your choice. Repeat this configuration for each
+EFS instance that you want to use in your pipeline.
+
+You can then use an EFS instance as the work directory based on its mount path:
+
+```groovy
+workDir = '/mnt/efs'
 ```
 
-In the above snippet replace `efs-1234567890` with the ID of your EFS instance and 
-the path `/mnt/fsx` with one of your choice. 
+Available options:
 
-Repeat the above configuratio for all file system instance you want to configure 
-in your pipeline. 
+`aws.batch.efsVolumes.'<ID>'.mountPath`
+: The host path to which the file system should be made available (default: none)
 
+`aws.batch.efsVolumes.'<ID>'.rootPath`
+: The file system directory that should be made available through the mount point (default: `/`) 
 
-| Config option 	                  | Description 	              |
-|---	                              |---	                        |
-| `aws.batch.efsVolumes.'<ID>'.mountPath`  | The host path to which the file system should be made available (default: none )
-| `aws.batch.efsVolumes.'<ID>'.rootPath`   | The file system directory that should be made available throught the mount point (optional, default: `/`) 
-| `aws.batch.efsVolumes.'<ID>'.readOnly`   | When `true` only allows the read of files (optional, default: `false`)
+`aws.batch.efsVolumes.'<ID>'.readOnly`
+: When `true` mounts the file system as read-only (default: `false`)
 
-Note: Replace the `<ID>` placeholder in the above table with your EFS file system identifier.  
+*Note: Replace `<ID>` with your EFS instance ID.*
 
-## Use of a POSIX-based shared file-system 
+## Using a POSIX-based shared file-system
 
-Using `xpack-amzn` plugin you can use any POSIX-based shared file-system, along with 
-AWS Batch such as [AWS FSx](https://aws.amazon.com/fsx/), [Qumolo](https://qumulo.com/), [Weka](https://www.weka.io/), etc.
+With the `xpack-amzn` plugin, you can use any POSIX-based shared file-system with 
+AWS Batch, such as [Amazon FSx](https://aws.amazon.com/fsx/), [Qumolo](https://qumulo.com/), [Weka](https://www.weka.io/), etc.
 
-The configuration of such file systems is out of the scope of this guide and it's 
-expected to be managed by the user. 
+The provisioning and management of such file systems are your responsibility. Typically,
+these file systems must be mounted in the launch template used to execute tasks.
 
-To use this file system as work directory in your Nextflow pipeline execution, 
-you will only need to specify a shared directory path in the Nextflow command-line 
-with the `-w` option, e.g. 
+As with EFS, you can then use the shared file system as the work directory based on its mount path:
 
-```
-nextflow run <MY-PIPELINE> -w /mnt/some/shared/dir
+```groovy
+workDir = '/mnt/fsx'
 ```
 
-To access shared file paths, other than the pipeline work directory, it is required to 
-declare such file or directory paths using the Nextflow `volumes` configuration 
-option as described as [this link](https://www.nextflow.io/docs/latest/awscloud.html#volume-mounts).
+You can also mount additional shared file systems into the task containers with the `aws.batch.volumes`
+config option. See the [Nextflow documentation](https://nextflow.io/docs/latest/aws.html#volume-mounts)
+for more details.