docs: added more informative CL messages (#18)

*fixes typo in the help messages

workflow/cli_utils.py

@@ -75,8 +75,8 @@ def show_help_message():
         "\n    kgwasflow test -t 16 -n"
         "\n\n2. Run the kGWASflow test using the test config file with 16 threads:\n"
         "\n    kgwasflow test -t 16"
-        "\n\n3. Run the kGWASflow test and define the test output folder:\n"
-        "\n    kgwasflow test -t 16  --output path/to/test_output_dir"
+        "\n\n3. Run the kGWASflow test and define the working directory:\n"
+        "\n    kgwasflow test -t 16 --work-dir path/to/test_output_dir"
     )
     return message
 

workflow/kgwasflow.py

@@ -52,6 +52,14 @@ def run(snakefile, config_file, **kwargs):
 @click.command(epilog=show_help_message(), context_settings=dict(help_option_names=["-h", "--help"], ignore_unknown_options=True))
 def test(snakefile, config_file, **kwargs):
     """Test kGWASflow workflow."""
+
+    click.secho("Starting kGWASflow test using the E.coli dataset...", fg="yellow")
+    click.secho("\nFor detailed info on this test, visit: ", fg="yellow", nl=False)
+    click.secho("https://github.com/akcorut/kGWASflow#testing", fg="blue", underline=True)
+
+    if kwargs.get('dryrun', False):
+        click.secho("\n[WARNING] This is a dryrun (flag -n or --dryrun was used)!\n", fg="magenta")
+
     if not snakefile:
         snakefile = get_snakefile()
 
@@ -72,6 +80,8 @@ def test(snakefile, config_file, **kwargs):
 def init_workdir(work_dir):
     """Initialize a new kGWASflow working directory with default configuration files."""
 
+    click.secho("Initializing a new kGWASflow working directory... Won't take long!", fg="yellow")
+
     config_file = get_configfile() # Get the default config.yaml file
     sample_file = get_samplefile() # Get the default samples.tsv file
     phenos_file = get_phenosfile() # Get the default phenos.tsv file
@@ -89,11 +99,21 @@ def init_workdir(work_dir):
         os.makedirs(work_dir)
     if not os.path.exists(config_path):
         os.makedirs(config_path)
-
+        
     copyfile(config_file, config_yaml_path)
+    click.secho("\n[INFO] Config.yaml file has been created at: " + config_yaml_path, fg="cyan")
+
     copyfile(sample_file, samples_tsv_path)
+    click.secho("[INFO] Samples.tsv file has been created at: " + samples_tsv_path, fg="cyan")
+
     copyfile(phenos_file, phenos_tsv_path)
+    click.secho("[INFO] Phenos.tsv file has been created at: " + phenos_tsv_path, fg="cyan")
+
     shutil.copytree(test_dir, new_test_dir, dirs_exist_ok=True)
+    click.secho("[INFO] Test directory has been created at: " + new_test_dir, fg="cyan")
+
+    click.secho("\nSuccess! kGWASflow initialization is complete! You can now run the workflow with:", fg="green")
+    click.secho("\nkgwasflow run (...)\n", fg="blue", bold=True)
 
 cli.add_command(run)
 cli.add_command(test)