updated indentation

src/software/automation_pipeline_developer.md

@@ -44,20 +44,20 @@ The class that manages workflow at the recording level is (<a href="https://gith
 
 + **recording_status_dict** in (<a href="https://github.com/BrainCOGS/U19-pipeline_python/blob/master/u19_pipeline/automatic_job/params_config.py">Params Config file</a>): This dictionary defines status definitions and corresponding functions to execute.
 + **pipeline_handler_main** in (<a href="https://github.com/BrainCOGS/U19-pipeline_python/blob/master/u19_pipeline/automatic_job/u19_pipeline/automatic_job/recording_handler.py">RecordingHandler</a>): Main function in recording workflow
-1. Executes corresponding functions based in status.
-2. Executed every 30 minutes to check for new recordings to be handled.
-3. Send notifications for processed and failed functions.
-+  **exception_handler** in (<a href="https://github.com/BrainCOGS/U19-pipeline_python/blob/master/u19_pipeline/automatic_job/u19_pipeline/automatic_job/recording_handler.py">RecordingHandler</a>): Python decorator for error handling.
+  1. Executes corresponding functions based in status.
+  2. Executed every 30 minutes to check for new recordings to be handled.
+  3. Send notifications for processed and failed functions.
+  +  **exception_handler** in (<a href="https://github.com/BrainCOGS/U19-pipeline_python/blob/master/u19_pipeline/automatic_job/u19_pipeline/automatic_job/recording_handler.py">RecordingHandler</a>): Python decorator for error handling.
 +  **modality_preingestion** in (<a href="https://github.com/BrainCOGS/U19-pipeline_python/blob/master/u19_pipeline/automatic_job/u19_pipeline/automatic_job/recording_handler.py">RecordingHandler</a>): Main ingestion function from recording to recording_process tables. There are subcalls depending on modality of recording (ephys or imaging).
 
 #### Imaging preingestion main steps:
 
 +  **imaging_preingestion** in (<a href="https://github.com/BrainCOGS/U19-pipeline_python/blob/master/u19_pipeline/automatic_job/u19_pipeline/automatic_job/recording_handler.py">RecordingHandler</a>): Ingestion to recording_process table for an imaging recording. Get all FOVs (TIFF stacks) for the recording and assign a new job for each one with corresponding parameters fetched from selection done in automation GUI.
 **AcquiredTiff populate function** in (<a href="https://github.com/BrainCOGS/U19-pipeline_python/blob/master/u19_pipeline/imaging_pipeline.py">Imaging pipeline</a>): Auxiliar script to call **populate_Imaging_AcquiredTiff** script in MATLAB.
 + **populate_Imaging_AcquiredTiff** in (<a href="https://github.com/BrainCOGS/U19-pipeline-matlab/blob/master/scripts/populate_Imaging_AcquiredTiff.m">populate_Imaging_AcquiredTiff</a>): Population calls to:
-1. **u19_imaging_pipeline.AcquiredTiff**: Each recording is divided into Tiff Splits (e.g. Mesoscope recordings contain multiple tiff stacks that will be processed independently). (<a href="https://github.com/BrainCOGS/U19-pipeline-matlab/blob/master/schemas/%2Bimaging_pipeline/AcquiredTiff.m">Code here</a>)
-2. **u19_imaging_pipeline.SyncImagingBehavior**: Find correspondence between virtual reality frame in the behavior experiment and Calcium Imaging frame in recording.
-(<a href="https://github.com/BrainCOGS/U19-pipeline-matlab/blob/master/schemas/%2Bimaging_pipeline/SyncImagingBehavior.m">Code here</a>)
+  1. **u19_imaging_pipeline.AcquiredTiff**: Each recording is divided into Tiff Splits (e.g. Mesoscope recordings contain multiple tiff stacks that will be processed independently). (<a href="https://github.com/BrainCOGS/U19-pipeline-matlab/blob/master/schemas/%2Bimaging_pipeline/AcquiredTiff.m">Code here</a>)
+  2. **u19_imaging_pipeline.SyncImagingBehavior**: Find correspondence between virtual reality frame in the behavior experiment and Calcium Imaging frame in recording.
+  (<a href="https://github.com/BrainCOGS/U19-pipeline-matlab/blob/master/schemas/%2Bimaging_pipeline/SyncImagingBehavior.m">Code here</a>)