ci 821 update documentation (#172)

* add pipeline configuration documentation

* allow running create-pipeline-config with no options

---------

Co-authored-by: Lee Pang <[email protected]>

Author: wleepang

README.md

@@ -17,6 +17,16 @@ or you can install the main branch of the repo by running:
 
 `pip install git+https://github.com/CirroBio/Cirro-client.git`
 
+To enable [pipeline configuration](#configuring-a-pipeline) you need to install extras using:
+
+```bash
+pip install cirro[nextflow]      # just nextflow pipeline configuration support
+pip install cirro[wdl]           # just wdl pipeline configuraiton support
+pip install cirro[nextflow,wdl]  # both nextflow and wdl pipeline configuration support
+```
+
+**NOTE**: Configuring Nextflow pipelines also requires a local installation of [`nextflow`](https://www.nextflow.io/).
+
 ## Authentication
 
 Upon first use, the Cirro client will ask you what Cirro instance to use and if you would like to save your login information.
@@ -99,6 +109,28 @@ Options:
   --help                 Show this message and exit.
 ```
 
+#### Configuring a pipeline
+```bash
+Usage: cirro create-pipeline-config [OPTIONS]
+
+  Create pipeline configuration files
+
+Options:
+  -p, --pipeline-dir DIRECTORY  Directory containing the pipeline definition
+                                files (e.g., WDL or Nextflow)  [default: .]
+  -e, --entrypoint TEXT         Entrypoint WDL file (optional, if not
+                                specified, the first WDL file found will be
+                                used). Ignored for Nextflow pipelines.
+  -o, --output-dir TEXT         Directory to store the generated configuration
+                                files  [default: .cirro]
+  -i, --interactive             Gather arguments interactively
+  --help                        Show this message and exit.
+```
+
+It is highly recommended that:
+- Nextflow pipelines utilize a [`nextflow_schema.json`](https://nextflow-io.github.io/nf-schema/latest/nextflow_schema/nextflow_schema_specification/) file. (If your pipeline originates from [NF-Core](https://nf-co.re/), this should already be the case.)
+- WDL pipelines are defined in WDL v1.0 or higher and explicitly define an `input` section in the root-level workflow.
+
 ### Interactive Commands
 
 When running a command, you can specify the `--interactive` flag to gather the command arguments interactively.

cirro/cli/cli.py

@@ -104,9 +104,8 @@ def configure():
     run_configure()
 
 
-@run.command(help='Create pipeline configuration files', no_args_is_help=True)
+@run.command(help='Create pipeline configuration files')
 @click.option('-p', '--pipeline-dir',
-              required=True,
               metavar='DIRECTORY',
               help='Directory containing the pipeline definition files (e.g., WDL or Nextflow)',
               default='.',
@@ -117,7 +116,7 @@ def configure():
                   ' Ignored for Nextflow pipelines.'),
               default='main.wdl')
 @click.option('-o', '--output-dir',
-              help='Directory to store the generated configuration files (default: current directory)',
+              help='Directory to store the generated configuration files',
               default='.cirro',
               show_default=True)
 @click.option('-i', '--interactive',