deactivate bed file input text when not required

Author: msarkis-icr

custom_files/pipeline_project_map_specifications.yaml

@@ -1,12 +1,16 @@
 epi2me-human-variation:
   nf-long-reads:
     is_inputType_path: False
+    bed_file_as_arg: True
 epi2me-basecalling:
   genomrep-support:
-    is_inputType_path: True  
+    is_inputType_path: False
+    bed_file_as_arg: False
 epi2me-somatic-variation:
   mopopgen-support:
     is_inputType_path: True
+    bed_file_as_arg: False
 nfcore-rnaseq:
   nf-tp53:
     is_inputType_path: True
+    bed_file_as_arg: False

pages/run_pipeline.py

@@ -35,7 +35,7 @@ def reset_button_state():
 button_clicked = ss_values["button_clicked"]
 custom_sample_list = ss_values["custom_sample_list"]  # only availanle if custom sample is selected
 BED_FILE = ss_values["BED_FILE"]
-samples = ["all", "demo", "customised"]  # , "test"]
+samples = ["demo", "customised"]  # , "test"]
 
 # Create the selectbox and update session state
 pipeline_options = ["select"] + list(map_pipeline_project.keys())
@@ -73,11 +73,14 @@ def reset_button_state():
 
             st.write("Your custom samples:", custom_sample_list)
             ss_set("custom_sample_list", custom_sample_list)
+    
+    use_bed_file = map_pipeline_project[PIPELINE][PROJECT]["bed_file_as_arg"]#bool
     # Optional BED file path
     BED_FILE = st.text_input(
         "Optional BED file path",
         value="",
         help="Provide a full path to a BED file on Alma server, or leave empty to skip and use full genome",
+        disabled=not use_bed_file
     )
 WORK_DIR = st.text_input("Working directory", value=WORK_DIR or SCRATCH)
 OUTPUT_DIR = st.text_input("Output directory", value=OUTPUT_DIR or SCRATCH)

tabs/tab_logon.py

@@ -64,20 +64,26 @@ def update_group():
                 "GROUP": ss_get("group_selection"),
                 "SCRATCH": SCRATCH,
                 "RDS": RDS,
+                "WORK_DIR": SCRATCH,
+                "OUTPUT_DIR": SCRATCH,  # set default to scratch
             }
         )
 
     def create_radio(GROUPS):
         options = GROUPS if GROUPS else []
         selection = ss_get("group_selection")
         index = options.index(selection) if selection in options else 0
+        # Force initialize session_state manually if only one option
+        if len(options) == 1:
+            ss_set("temp_group_selection",options[0])
+            update_group()
 
         st.radio(
             "Select group",
             options,
             index=index,
             key="temp_group_selection",  # Temporary key for updates
-            on_change=update_group,  # Calls update function on change
+            on_change=update_group, # Calls update function on change
         )
 
     # Handle connection
@@ -101,10 +107,6 @@ def create_radio(GROUPS):
             "password": password,
             "GROUP": GROUP,
             "GROUPS": GROUPS,
-            "SCRATCH": SCRATCH,
-            "WORK_DIR": SCRATCH,
-            "OUTPUT_DIR": SCRATCH,  # set default to scratch
-            "RDS": RDS,
             "SAMPLE": SAMPLE,
             "PIPELINE": PIPELINE,
             "PROJECT": PROJECT,