add processes 2 remove option

bioflow_insight_cli/main.py

@@ -16,9 +16,18 @@ from src.workflow import Workflow
     default=False,
     is_flag=True,
     help=''
-    'When processes and subworkflows are duplicated in the workflows by the \'include as\' option, '
-    'this option will duplicate the procedures in the graph output.',
+    'When processes and subworkflows are duplicated in the workflow by the \'include as\' option, '
+    'this option will duplicate the task in the graph output.',
 )
+
+@click.option(
+    '--processes-to-remove',
+    'processes_2_remove',
+    required=False,
+    help=''
+    'List of processes which are to be removed from the different structural representations (format "process1, process2, ...").',
+)
+
 @click.option(
     '--render-graphs',
     'render_graphs',
@@ -36,13 +45,13 @@ from src.workflow import Workflow
     'authors',
     required=False,
     help=''
-    'Authors of workflow (format "author1, author2, ..."),'
+    '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('--date-published', 'datePublished', required=False, help='Publication date (format "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).')

src/workflow.py

@@ -14,7 +14,7 @@ class Workflow:
                  name = None, datePublished=None, description=None,
                  license = None, creativeWorkStatus = None, authors = None, 
                  version = None, keywords = None, producer = None,
-                 publisher = None):
+                 publisher = None, processes_2_remove = None):
         self.nextflow_file = Nextflow_File(
             file,
             duplicate=duplicate,
@@ -33,6 +33,7 @@ class Workflow:
         self.keywords = keywords
         self.producer = producer
         self.publisher = publisher
+        self.processes_2_remove = processes_2_remove
         self.log = ""
         self.fill_log()
         self.address = ""
@@ -213,5 +214,10 @@ class Workflow:
         self.nextflow_file.initialise()
         self.initialise_rocrate()
 
-    def generate_all_graphs(self, render_graphs = True, processes_2_remove = []):
-        self.nextflow_file.generate_all_graphs(render_graphs = render_graphs, processes_2_remove = processes_2_remove)
+    def generate_all_graphs(self, render_graphs = True):
+        tab_processes_2_remove = []
+        if(self.processes_2_remove!=None):
+            temp = self.processes_2_remove.split(",")
+            for t in temp:
+                tab_processes_2_remove.append(t.strip())
+        self.nextflow_file.generate_all_graphs(render_graphs = render_graphs, processes_2_remove = tab_processes_2_remove)