Update README.md

README.md

@@ -6,7 +6,6 @@ Runs on files produced by [sf-daq](https://github.com/paulscherrerinstitute/sf_d
 
 # Table of Contents
 * [Installation](#installation)
-* [Google Authentication](#google-api)
 * [Usage](#usage)
    * [Before beamtime](#usage1)
    * [During beamtime](#usage2)
@@ -16,6 +15,7 @@ Runs on files produced by [sf-daq](https://github.com/paulscherrerinstitute/sf_d
        * [pausing indexing](#usage2_pause)
    * [After beamtime](#usage3)
 * [Configuration files](#config)
+* [Google Authentication](#google-api)
 
 ## Description
 Automatic Processing tool checks for the new files/runs produced by sf-daq and runs automatically workload (currently - indexing (by crystfel)) and fills logbook (google spreadsheet) with information with some daq parameters from the sf-daq and processing.
@@ -42,7 +42,7 @@ Needed conda environment can be sourced/used from the common place. In case new
 gspread numpy matplotlib
 ```
 
-In case of installation from source, so different location of the code and conda environment - change correspondingly lines in [env_setup.sh](#config_env_setup) file 
+In case of installation from source, so different location of the code or conda environment - change correspondingly lines in [env_setup.sh](#config_env_setup) file 
 
 ## Google Authentication<a name="google-api"></a>
 
@@ -208,6 +208,11 @@ this file contains indexing parameters used by crystfel.
 
 **HINT** - in case several proteins are used during expertiment, it's possible to define different indexing parameters for each of them: in case run_index.<cell_name>.sh file is present - indexing parameters from that file will be used to process <cell_name> protein sample, if not present(default) - run_index.sh parameters are used
 
+## Google Authentication<a name="google-api"></a>
+
+ ap can fill automatically google spreadsheet with different information. This is done using google-api and one need to have api-keys created and allowed for the corresponding spreadsheet (logbook). To create keys, few steps needs to be done first:  
+- [enable API access for a project](https://docs.gspread.org/en/v5.10.0/oauth2.html#enable-api-access-for-a-project) 
+- [create (*hint* - do several for same project) service accounts](https://docs.gspread.org/en/v5.10.0/oauth2.html#for-bots-using-service-account) (steps 1-4)
 
 ## Roadmap
 
@@ -218,4 +223,6 @@ this file contains indexing parameters used by crystfel.
 ## Authors and acknowledgment
 Automatic Processing tool was made in 2018 by Karol Nass and Dmitry Ozerov. 
 
+Automatic processing pipeline is described in "*Nass, K. et al. Pink-beam serial femtosecond crystallography for accurate structure-factor determination at an X-ray free-electron laser. IUCrJ 8, 905–920 (2021).*" This paper can be referenced in case usage of automatic pipeline was helpful in beamtime.
+