Update readme

scripts/README.md

@@ -49,3 +49,58 @@ In this command:
 - `tmp-fg` is the filegroup slug to which files should be copied.
 - `12345` is the ID of the request for which the files belong.
 - `runId=ABCD_123 runMode="XSeq"` are optional key-value pairs that can be added as metadata when copying files.
+
+## parse_cohort_files.py  
+This script is typically used before submitting Tempo Jobs for alignment.    
+There are three commands in this script.  
+-`Parse` Creates the input file to run Tempo jobs by comparing the cohort directory with bams and parsing the differences.  
+-`Check` Creates a script to check if files exist.   
+-`Remove` Creates a scripts which deletes the files.  
+
+Usage:  
+
+Prerequisite:  
+
+    Switch to tempobot for access to cohort directory:
+         source /usersoftware/core006/dodzdo.sh  
+
+    Activate conda environment:  
+         conda activate py37  
+
+    Set enviornment variables:
+        - BEAGLE_USER
+        - BEAGLE_PW
+        - BEAGLE_ENDPOINT
+
+Here is an example for parse_cohort_files.py *parse* command:
+```
+
+python3 parse_cohort_files.py parse <input_files> <directory_path> <parse_output> <diff_output> [<file_group_id>]
+    - <input_files> can be a single file, multiple files, or a wildcard (e.g., /path/to/files/*.txt)
+    - <directory_path> is the path containing existing directories to compare  
+
+python3 parse_cohort_files.py parse /data1/core006/ccs_pipelines/tempo/wes_repo/Results/v2.1.x/cohort_level/*.txt /data1/core006/ccs_pipelines/tempo/wes_repo/Results/v2.1.x/bams/ parse_output.txt diff_output.txt
+```
+Here is an example for parse_cohort_files *check* command:
+```
+python3 parse_cohort_files.py check <input> <output>  
+
+python3 parse_cohort_files.py check CCS_F00000.cohort.txt CCS_F00000.cohort.check.sh
+```
+Here is an example for parse_cohort_files *remove* command:
+```
+python3 parse_cohort_files.py remove <input> <output>
+
+python3 parse_cohort_files.py remove CCS_F00000.cohort.txt CCS_F00000.cohort.remove_file.sh
+```
+## submit_tempo_jobs.py  
+
+The submit_tempo_jobs.py script is used to submit tempo jobs to voyager using the <diff_output> file created from the parse command.
+
+Here is a usage example of submit_tempo_jobs:
+
+```
+python submit_tempo_jobs.py diff_output.txt CCS_F00000  
+
+python submit_tempo_jobs.py <diff_output> <cohort_id> [<job_group_id>]
+```

scripts/parse_cohort_files.py

@@ -136,38 +136,44 @@ def parse_cohort_file(input_files, directory_path, output_file, diff_output_file
 python3 parse_cohort_files.py parse <input_files> <directory_path> <parse_output> <diff_output> [<file_group_id>]
     - <input_files> can be a single file, multiple files, or a wildcard (e.g., /path/to/files/*.txt)
     - <directory_path> is the path containing existing directories to compare
-python3 parse_cohort_files.py remove <input> [<output>]
-python3 parse_cohort_files.py check <input> [<output>]
-python3 parse_cohort_files.py list_dir <directory> [<output>]
-python3 parse_cohort_files.py compare <file1.txt> <file2.txt> <report_file>
+python3 parse_cohort_files.py remove <input> <output>
+python3 parse_cohort_files.py check <input> <output>
 
 """
 
 if __name__ == "__main__":
-    if len(sys.argv) < 6:
+    if len(sys.argv) < 2:
         print(HELP)
         exit(1)
     command = sys.argv[1]
     if command == "parse":
+        if len(sys.argv) < 6:
+            print(HELP)
+            exit(1)
         input_files = sys.argv[2:-3] 
         directory_path = sys.argv[-3]
         output_file = sys.argv[-2]   
         diff_output_file = sys.argv[-1] 
         parse_cohort_file(input_files, directory_path, output_file, diff_output_file)
     elif command == "remove":
+        if len(sys.argv) != 4:
+            print(HELP)
+            exit(1)
         input_file = sys.argv[2]
         if len(sys.argv) > 2:
             output_file = sys.argv[3]
             create_remove_script(input_file, output_file)
         else:
             create_remove_script(input_file)
     elif command == "check":
+        if len(sys.argv) != 4:
+            print(HELP)
+            exit(1)
         input_file = sys.argv[2]
         if len(sys.argv) > 2:
             output_file = sys.argv[3]
             create_check_script(input_file, output_file)
         else:
             create_check_script(input_file)   
     else:
-        print(HELP)
-
+        print(HELP)