Minor changes

docs/quickstart_guide.md

@@ -7,7 +7,7 @@ This suite will be named `efas_report` and its code will live in a directory nam
 `projects`.
 
 ```shell
-$ wellies-quickstart -p efas_report ~/projects/efas_report
+$ wellies-quickstart ~/projects/efas_report -p efas_report
 $ cd ~/projects/efas_report
 ```
 
@@ -101,7 +101,7 @@ configs/
 
 For a quick overview of what these files do:
 
-- `config.yaml` - handles the [pyflow](https://github.com/ecmwf/pyflow) suite and repository
+- `config.yaml` - handles the main options of the suite (paths, hosts, user, etc.)
 - [`data.yaml`](./config/data_config.md) - configuration of data retrieval and handling
 - [`execution_contexts.yaml`](./config/exec_config.md) - for configuring how tasks are executed on hosts and queueing systems such as SLURM 
 - [`tools.yaml`](./config/tools_config.md) - for conda environment creation and loading, environment variable handling etc
@@ -113,8 +113,7 @@ To start, let's take a look at `config.yaml`
 
 ### `config.yaml`
 
-As mentioned above, this file handles the configuration of the [pyflow](https://github.com/ecmwf/pyflow) suite and repository
-in which the suite is stored. We'll start with the minmial example generated by wellies.
+As mentioned above, this file handles the main options of the suite. We'll start with the minmial example generated by wellies.
 
 ```yaml title="config.yaml"
 # Configuration file for pyflow suite.
@@ -136,13 +135,13 @@ in which the suite is stored. We'll start with the minmial example generated by
 suite_name: "efas_report"
 hostname: "localhost"
 user: "{USER}"
+workdir: "$TMPDIR"
+output_root: "{SCRATCH}/efas_report"
 
 # example options
 deploy_dir: "{PERM}/pyflow/efas_report"
 job_out: "%ECF_HOME%"
-workdir: "$TMPDIR"
 
-output_root: "{SCRATCH}/efas_report"
 
 # ---------- Specific optionals -----------------------------------------------
 # add your project's specific variables and options here
@@ -153,15 +152,15 @@ To break down the configuration settings:
 #### Host options
 
 - `suite_name` - the name of the suite
-- `hostname` - the host on which we want the suite to run, such as our HPC cluster
-- `user` - by default `{USER}` will be replaced with our username, it should be set to your username on the HPC system running the suite
+- `hostname` - the host on which we want the suite to run, typically the hostname of the HPC
+- `user` - by default `{USER}` will be replaced with your local username, it should be set to your username on the HPC system running the suite
+- `workdir` - the working directory where the tasks will run on the HPC by default (for read/write purposes)
+- `output_root` - a folderpath used for storage of tools, Python environments and static data stores
 
 #### Suite options
 
-- `deploy_dir` - where the main suite files and git repo will be created, `/perm/username/pyflow/efas_report` above
-- `job_out` - job output directory, where files should be created
-- `workdir` - a temporary working directory read/write purposes
-- `output_root` - a folderpath used for storage of tools, Python environments and static data stores
+- `deploy_dir` - where the main suite files (and git repo tracking the deployment) will be created, in this case `/perm/username/pyflow/efas_report`
+- `job_out` - job output directory, where files related to the jobs will be created (logs, submission scripts, etc.)
 
 Let's update the configuration to use a fixed username