add ellie wright; Add new arg for nanopore-pauses

Author: msarkis-icr

custom_files/user_whitelist.tsv

@@ -6,3 +6,4 @@ sstephens	dgeraeach	None
 jhouseham	UNKNOWN	None
 ahyde1	MOPOPGEN	None
 bdelpino	dbiphdaer	None
+ewright	dbiphdaer	None

pages/run_pipeline.py

@@ -31,7 +31,7 @@ def reset_button_state():
 JOB_ID = ss_values["JOB_ID"]
 WORK_DIR = ss_values["WORK_DIR"]
 OUTPUT_DIR = ss_values["OUTPUT_DIR"]
-BAM_DIR = ss_values["BAM_DIR"]
+IN_DIR = ss_values["IN_DIR"]
 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
@@ -92,7 +92,15 @@ def reset_button_state():
     )
 WORK_DIR = st.text_input("Working directory", value=WORK_DIR or SCRATCH)
 OUTPUT_DIR = st.text_input("Output directory", value=OUTPUT_DIR or SCRATCH)
-BAM_DIR = st.text_input("Adapted BAM directory", value=BAM_DIR or "/data/rds/DGE/DUDGE/OGENETIC/Data/Nanopore/samples")
+
+# very specific field for default values that I would like to remove
+default_path = ""
+if PIPELINE == "icr-nanopore-pauses" and PROJECT == "genomrep-support":
+    default_path = "/data/rds/DBI/DUDBI/GENOMREP/bdelpino/Nanopore\ Sequencing/Raw\ data/250506_K562_AvsS/no_sample_id"
+elif PROJECT == "nf-long-reads":
+    default_path = "/data/rds/DGE/DUDGE/OGENETIC/Data/Nanopore/samples"
+
+IN_DIR = st.text_input("Sample directory", value=IN_DIR or default_path)
 
 dry_run = st.checkbox("Dry run (do not execute the job)", value=False)
 
@@ -106,7 +114,7 @@ def reset_button_state():
         selected_samples=SAMPLE,
         work_dir=WORK_DIR,
         output_dir=OUTPUT_DIR,
-        bam_dir=BAM_DIR,
+        bam_dir=IN_DIR, # not always bam files, TODO: rename it
         custom_sample_list=custom_sample_list,
         bed_file=BED_FILE,
         dry_run=dry_run,
@@ -129,7 +137,7 @@ def reset_button_state():
             # "JOB_ID": JOB_ID,
             "WORK_DIR": WORK_DIR,
             "OUTPUT_DIR": OUTPUT_DIR,
-            "BAM_DIR": BAM_DIR,
+            "IN_DIR": IN_DIR,
             "run_pipeline_clicked": run_pipeline_clicked,
             "button_clicked": button_clicked,
             "custom_sample_list": custom_sample_list,

shared/command_helper.py

@@ -30,7 +30,7 @@ def pipe_cmd(
     selected_samples="",
     work_dir="work",
     output_dir="output",
-    bam_dir="",
+    bam_dir="",# it s not always a bam dir, depending on the pipeline
     custom_sample_list=[],
     bed_file="",
     dry_run=False,
@@ -58,8 +58,13 @@ def get_pipeline_command():
                 "--work-dir", work_dir,
                 "--outdir", output_dir,
                 "--samples", " ".join(custom_sample_list),
-                "--out_bam_folder", bam_dir,
+                #"--out_bam_folder", bam_dir,
             ]
+            if selected_pipeline == "icr-nanopore-pauses" and selected_project == "genomrep-support":
+                args+= ["--base-dir", bam_dir]
+            elif selected_project == "nf-long-reads":
+                args+= ["--out_bam_folder", bam_dir]
+
             if adapt_samples:
                 args += ["--adapt-samples"]
             if bed_file:
@@ -69,7 +74,11 @@ def get_pipeline_command():
         preamble = f"""
         mkdir -p {work_dir}/logs
         cd {work_dir}
-        mkdir {bam_dir}
+        """
+
+        if selected_project == "nf-long-reads":
+            preamble += f"""
+        mkdir -p {bam_dir}
         """
         # Combine all into the final shell command
         cmd_pipeline = preamble + f"{base_cmd} {' '.join(args)}"

shared/ss_defaults.yaml

@@ -19,4 +19,4 @@ keys_defaults:
   OUTPUT_DIR: None
   custom_sample_list: []
   BED_FILE: ""
-  BAM_DIR: ""
+  IN_DIR: ""