final fixes

Author: msarkis-icr

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 = ["demo", "customised"]  # , "test"]
+samples = ["demo", "customised"]
 
 # Create the selectbox and update session state
 pipeline_options = ["select"] + list(map_pipeline_project.keys())

shared/command_helper.py

@@ -1,5 +1,5 @@
 import os
-from typing import Tuple, Optional
+import streamlit as st
 
 def get_path_to_script(
     selected_pipeline: str,
@@ -27,7 +27,7 @@ def pipe_cmd(
     selected_pipeline="",
     selected_project="",
     cmd_num=0,
-    selected_samples="all",
+    selected_samples="",
     work_dir="work",
     output_dir="output",
     custom_sample_list=[],
@@ -74,16 +74,16 @@ def get_pipeline_command():
 
     # Command mappings
     command_map = {
-        0: get_pipeline_command(),
-        1: f"squeue -u {username}",
-        2: (
+        0: get_pipeline_command,
+        1: lambda: f"squeue -u {username}",
+        2: lambda: (
             f"sacct --user {username} "
             "--format UID,User,JobID,JobName,Submit,Elapsed,Partition,"
             "NNodes,NCPUS,TotalCPU,CPUTime,ReqMem,MaxRSS,WorkDir,State,"
             "Account,AllocTres -P"
         ),
-        3: "echo hello from nextflow-on-Alma app",
+        3: lambda: "echo hello from nextflow-on-Alma app",
     }
 
     # Return the corresponding command
-    return command_map.get(cmd_num, "echo 'Invalid command number'")
+    return command_map.get(cmd_num, lambda: "echo 'Invalid command number'")()

tabs/tab_command.py

@@ -102,6 +102,7 @@ def run_nextflow():
     with tabQ:
         if st.button("Check slurm queues"):
             output = st.empty()
+            st.write(cmd_hlp.pipe_cmd(st.session_state["username"], cmd_num=1))
             with st.spinner("Checking queue..."):
                 with hlp.st_capture(output.code):
                     cmd_pipeline = cmd_hlp.pipe_cmd(st.session_state["username"], cmd_num=1)