update parameters

bioflow_insight_cli/main.py

@@ -7,23 +7,6 @@ from src.workflow import Workflow
 @click.command()
 @click.version_option(bioflow_insight_src.__version__)
 @click.argument('main_workflow_path')
-@click.option('--name', 'name', required=False, help='Workflow name, extracted otherwise (in the case of a Git repo).')
-@click.option('--date-published', 'datePublished', required=False, help='Publication date ("yyyy-mm-dd"), extracted otherwise (in the case of a Git repo).')
-@click.option('--description', 'description', required=False, help='Description of workflow, extracted otherwise (in the case of a Git repo).')
-@click.option('--license', 'license', required=False, help='License of workflow, extracted otherwise (in the case of a Git repo).')
-@click.option('--creative-work-status', 'creativeWorkStatus', required=False, help='Creative work status of workflow, extracted otherwise (in the case of a Git repo).')
-@click.option('--version', 'version', required=False, help='Version of workflow, extracted otherwise (in the case of a Git repo).')
-@click.option('--keywords', 'keywords', required=False, help='Keywords of workflow (fomat "keyword1, keyword2, ..."), extracted otherwise (in the case of a Git repo).')
-@click.option('--producer', 'producer', required=False, help='Producer of workflow, extracted otherwise (in the case of a Git repo).')
-@click.option('--publisher', 'publisher', required=False, help='Publisher of workflow, extracted otherwise (in the case of a Git repo).')
-@click.option(
-    '--authors',
-    'authors',
-    required=False,
-    help=''
-    'Authors of workflow (format "[{\'@id\': "Author1", \'email\': "author1@email.com"}, ...]"), '
-    'extracted otherwise (in the case of a Git repo).',
-)
 
 @click.option('--output-dir', default='./results', help='Where the results will be written.')
 @click.option(
@@ -45,6 +28,30 @@ from src.workflow import Workflow
     help='Generate the graphs output in png format using graphviz (slower),'
     'the mermaid and dot formats are always generated.',
 )
+
+
+@click.option('--name', 'name', required=False, help='Workflow name, extracted otherwise (in the case of a Git repo).')
+@click.option(
+    '--authors',
+    'authors',
+    required=False,
+    help=''
+    'Authors of workflow (format "author1, author2, ..."),'
+    'extracted otherwise (in the case of a Git repo).',
+)
+
+@click.option('--keywords', 'keywords', required=False, help='Keywords of workflow (fomat "keyword1, keyword2, ..."), extracted otherwise (in the case of a Git repo).')
+@click.option('--description', 'description', required=False, help='Description of workflow, extracted otherwise (in the case of a Git repo).')
+@click.option('--date-published', 'datePublished', required=False, help='Publication date ("yyyy-mm-dd"), extracted otherwise (in the case of a Git repo).')
+
+@click.option('--license', 'license', required=False, help='License of workflow, extracted otherwise (in the case of a Git repo).')
+@click.option('--creative-work-status', 'creativeWorkStatus', required=False, help='Creative work status of workflow, extracted otherwise (in the case of a Git repo).')
+@click.option('--version', 'version', required=False, help='Version of workflow, extracted otherwise (in the case of a Git repo).')
+@click.option('--producer', 'producer', required=False, help='Producer of workflow, extracted otherwise (in the case of a Git repo).')
+@click.option('--publisher', 'publisher', required=False, help='Publisher of workflow, extracted otherwise (in the case of a Git repo).')
+
+
+
 @click.option(
     '--display-info',
     'display_info',
@@ -53,6 +60,7 @@ from src.workflow import Workflow
     is_flag=True,
     help='Option to show a visual summary of the analysis.',
 )
+
 def cli_command(main_workflow_path, **kwargs):
     return cli(main_workflow_path, **kwargs)
 

src/workflow.py

@@ -158,7 +158,11 @@ class Workflow:
                 tab.append({"@id":authors[author], "email":author})
             return tab
         else:
-            return self.authors
+            authors = authors.split(',')
+            tab = []
+            for a in authors:
+                tab.append({"@id":a.strip()})
+            return tab
     
 
     #Need to follow this format : "rna-seq, nextflow, bioinformatics, reproducibility, workflow, reproducible-research, bioinformatics-pipeline"