add bed file and make it optional

Author: msarkis-icr

pages/run_pipeline.py

@@ -34,7 +34,7 @@ def reset_button_state():
 run_pipeline_clicked = ss_values["run_pipeline_clicked"]
 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"]
 
 # Create the selectbox and update session state
@@ -73,7 +73,12 @@ def reset_button_state():
 
             st.write("Your custom samples:", custom_sample_list)
             ss_set("custom_sample_list", custom_sample_list)
-
+    # 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",
+    )
 WORK_DIR = st.text_input("Working directory", value=WORK_DIR or SCRATCH)
 OUTPUT_DIR = st.text_input("Output directory", value=OUTPUT_DIR or SCRATCH)
 
@@ -88,6 +93,7 @@ def reset_button_state():
         work_dir=WORK_DIR,
         output_dir=OUTPUT_DIR,
         custom_sample_list=custom_sample_list,
+        bed_file=BED_FILE
     )
     save_in_ss(
         {
@@ -109,6 +115,7 @@ def reset_button_state():
             "run_pipeline_clicked": run_pipeline_clicked,
             "button_clicked": button_clicked,
             "custom_sample_list": custom_sample_list,
+            "BED_FILE":BED_FILE,
         }
     )
 else:

shared/ss_defaults.yaml

@@ -18,3 +18,4 @@ keys_defaults:
   WORK_DIR: None
   OUTPUT_DIR: None
   custom_sample_list: []
+  BED_FILE: ""

tabs/tab_command.py

@@ -15,6 +15,7 @@ def tab(
     work_dir="work",
     output_dir="output",
     custom_sample_list=[],
+    bed_file=""
 ):
     # --- Initialize session state ---
     st.session_state.setdefault("username", username)
@@ -46,6 +47,7 @@ def run_nextflow():
             output_dir=output_dir,
             work_dir=work_dir,
             custom_sample_list=custom_sample_list,
+            bed_file=bed_file
         )
         st.code(cmd_pipeline)
         result = MY_SSH.run_cmd(cmd_pipeline)