fix_issue_16

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/command_helper.py

@@ -28,39 +28,52 @@ def pipe_cmd(
     work_dir="work",
     output_dir="output",
     custom_sample_list=[],
+    bed_file=""
 ):
     def get_pipeline_command():
         """Generate the pipeline execution command based on the sample selection."""
         path_to_script = get_path_to_script(selected_pipeline, selected_project, selected_samples)
 
-        cmd_pipeline = f"""
-        mkdir -p {work_dir}/logs
-        cd {work_dir}
-        """
         # not sure if this is the best thing-using job id for filenamne
         log_out = f"{work_dir}/logs/%j.out"
         log_err = f"{work_dir}/logs/%j.err"
 
+        args = []
+        base_cmd = f"sbatch -o {log_out} -e {log_err}"
+
         if selected_samples == "demo":
-            cmd_pipeline += f"sbatch  -o {log_out} -e {log_err} {path_to_script} {work_dir} {output_dir}"
-        elif selected_samples == "all":  # this has no more sense since we have to specify the sample name index
-            cmd_pipeline += f"sbatch  -o {log_out} -e {log_err} {path_to_script} --work-dir {work_dir} --outdir {output_dir}"
-            ##./your_script.sh --env "/my/custom/env" --work-dir "my_work" --outdir "my_output" --config "my_config" --params "parans.json"
-            # Usage:
-            # bash launch_batch_analysis.sh \
-            #     --work-dir "workdir" \
-            #     --outdir "output" \
-            #     --env "/data/rds/DIT/SCICOM/SCRSE/shared/conda/nextflow_env" \
-            #     --params "/data/params/parameters.json" \
-            #     --config "custom_config.config"
-        elif selected_samples == "customised":
-            if not len(custom_sample_list):
-                print("custom_sample_list cannot be empty")
+            args = [path_to_script, work_dir, output_dir]
 
-            tab_separated_string = "\t".join(custom_sample_list)
-            cmd_pipeline += f"sbatch  -o {log_out} -e {log_err} {path_to_script} --work-dir {work_dir} --outdir {output_dir} --samples {tab_separated_string}"
-        # elif selected_samples == "test":
+        elif selected_samples == "all":
+            #./your_script.sh --env "/my/custom/env" --work-dir "my_work" --outdir "my_output" --config "my_config" --params "parans.json" --bed file.bed
+            args = [
+                path_to_script,
+                "--work-dir", work_dir,
+                "--outdir", output_dir,
+            ]
+            if bed_file:
+                args += ["--bed", bed_file]
+
+        elif selected_samples == "customised":
+            if not custom_sample_list:
+                raise ValueError("custom_sample_list cannot be empty")
+            args = [
+                path_to_script,
+                "--work-dir", work_dir,
+                "--outdir", output_dir,
+                "--samples", "\t".join(custom_sample_list),
+            ]
+            if bed_file:
+                args += ["--bed", bed_file]
+        # elif selected_samples == "test": #this will become dry-run, but I should develop it for all scripts
         #     cmd_pipeline += f"sbatch  -o {log_out} -e {log_err} /data/scratch/DCO/DIGOPS/SCIENCOM/msarkis/NF-project-configurations/test.sh --work-dir {work_dir} --outdir {output_dir}"
+
+        preamble = f"""
+        mkdir -p {work_dir}/logs
+        cd {work_dir}
+        """
+        # Combine all into the final shell command
+        cmd_pipeline = preamble + f"{base_cmd} {' '.join(args)}"
         return cmd_pipeline.strip()
 
     # Command mappings

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)