Updated execution instructions for single and group running

docs/source/execution.rst

@@ -5,14 +5,77 @@ Running the Pipeline
 Running for a single dataset
 ============================
 
-::
+Run all single-dataset processes with the `single-run.py` script.
+```
 usage: single_run.py [-h] [-w WORKDIR] [-g GROUPDIR] [-G GROUPID] [-p PROJ_DIR] [-n NEW_VERSION] [-m MODE] [-t TIME_ALLOWED] [-b] [-s SUBSET] [-r REPEAT_ID] [-f] [-v] [-d] [-Q] phase proj_code
-::
 
-Required Parameters:
-:phase: Pipeline phase to execute
-:proj_code: Project code or ID for this dataset execution
+positional arguments:
+  phase                 Phase of the pipeline to initiate
+  proj_code             Project identifier code
+
+options:
+  -h, --help            show this help message and exit
+  -w WORKDIR, --workdir WORKDIR
+                        Working directory for pipeline
+  -g GROUPDIR, --groupdir GROUPDIR
+                        Group directory for pipeline
+  -G GROUPID, --groupID GROUPID
+                        Group identifier label
+  -p PROJ_DIR, --proj_dir PROJ_DIR
+                        Project directory for pipeline
+  -n NEW_VERSION, --new_version NEW_VERSION
+                        If present, create a new version
+  -m MODE, --mode MODE  Print or record information (log or std)
+  -t TIME_ALLOWED, --time-allowed TIME_ALLOWED
+                        Time limit for this job
+  -b, --bypass-errs     Bypass all error messages - skip failed jobs
+  -s SUBSET, --subset SUBSET
+                        Size of subset within group
+  -r REPEAT_ID, --repeat_id REPEAT_ID
+                        Repeat id (1 if first time running, <phase>_<repeat> otherwise)
+  -f                    Force overwrite of steps if previously done
+  -v, --verbose         Print helpful statements while running
+  -d, --dryrun          Perform dry-run (i.e no new files/dirs created)
+  -Q, --quality         Quality assured checks - thorough run
+```
 
 ===============================
 Running for a group of datasets
-===============================
+===============================
+
+Run all multi-dataset group processes within the pipeline using the `group_run.py` script.
+
+```
+usage: group_run.py [-h] [-s SOURCE] [-e VENVPATH] [-w WORKDIR] [-g GROUPDIR] [-p PROJ_DIR] [-n NEW_VERSION] [-m MODE] [-t TIME_ALLOWED] [-b] [-i INPUT] [-S SUBSET] [-r REPEAT_ID] [-f] [-v] [-d] [-Q] phase groupID
+
+positional arguments:
+  phase                 Phase of the pipeline to initiate
+  groupID               Group identifier code
+
+options:
+  -h, --help            show this help message and exit
+  -s SOURCE             Path to directory containing master scripts (this one)
+  -e VENVPATH           Path to virtual (e)nvironment (excludes /bin/activate)
+  -w WORKDIR, --workdir WORKDIR
+                        Working directory for pipeline
+  -g GROUPDIR, --groupdir GROUPDIR
+                        Group directory for pipeline
+  -p PROJ_DIR, --proj_dir PROJ_DIR
+                        Project directory for pipeline
+  -n NEW_VERSION, --new_version NEW_VERSION
+                        If present, create a new version
+  -m MODE, --mode MODE  Print or record information (log or std)
+  -t TIME_ALLOWED, --time-allowed TIME_ALLOWED
+                        Time limit for this job
+  -b, --bypass-errs     Bypass all error messages - skip failed jobs
+  -i INPUT, --input INPUT
+                        input file (for init phase)
+  -S SUBSET, --subset SUBSET
+                        Size of subset within group
+  -r REPEAT_ID, --repeat_id REPEAT_ID
+                        Repeat id (1 if first time running, <phase>_<repeat> otherwise)
+  -f                    Force overwrite of steps if previously done
+  -v, --verbose         Print helpful statements while running
+  -d, --dryrun          Perform dry-run (i.e no new files/dirs created)
+  -Q, --quality         Quality assured checks - thorough run
+```