Merge branch 'sync_in_wf' into 'dev'

Update README

See merge request !26

README.md

@@ -52,7 +52,8 @@ The "gga_load_data" tools are composed of 4 scripts:
 - gga_init: Create directory tree for organisms and deploy stacks for the input organisms as well as Traefik and optionally Authelia stacks
 - gga_get_data: Create `src_data` directory tree for organisms and copy datasets for the input organisms into `src_data`
 - gga_load_data: Load the datasets of the input organisms into their Galaxy library
-- run_workflow_phaeoexplorer: Remotely run a custom workflow in Galaxy, proposed as an "example script" to take inspiration from as workflow parameters are specific to the [Phaeoexplorer](https://phaeoexplorer.sb-roscoff.fr) data
+- gga_run_workflow_phaeo*: Multiple scripts to run custom workflows in Galaxy, proposed as "example scripts" to take inspiration from 
+  as workflow parameters are specific to the [Phaeoexplorer](https://phaeoexplorer.sb-roscoff.fr) data
 
 ## Usage:
 
@@ -68,31 +69,37 @@ in the `examples` folder.
 - Deploy stacks part: 
 
 ```bash
-$ python3 /path/to/repo/gga_init.py input_file.yml -c/--config config_file.yml [-v/--verbose] [OPTIONS]
-		--main-directory $PATH (Path where to create/update stacks; default=current directory)
-		--force-traefik (If specified, will overwrite traefik and authelia files; default=False)
+$ python3 /path/to/repo/gga_init.py input_file.yml \
+-c/--config config_file.yml \
+--main-directory $PATH (Path where to create/update stacks; default=current directory) \
+--force-traefik (If specified, will overwrite traefik and authelia files; default=False) \
+[-v/--verbose]
 ```
 
 - Copy source data file: 
 
 ```bash
-$ python3 /path/to/repo/gga_get_data.py input_file.yml [-v/--verbose] [OPTIONS]
-		--main-directory $PATH (Path where to access stacks; default=current directory)
+$ python3 /path/to/repo/gga_get_data.py input_file.yml \
+--main-directory $PATH (Path where to access stacks; default=current directory) \
+[-v/--verbose]
 ```
 
 - Load data in Galaxy library and prepare Galaxy instance: 
 
 ```bash
-$ python3 /path/to/repo/gga_load_data.py input_file.yml -c/--config config_file.yml [-v/--verbose]
-		--main-directory $PATH (Path where to access stacks; default=current directory)
+$ python3 /path/to/repo/gga_load_data.py input_file.yml \
+-c/--config config_file.yml \
+--main-directory $PATH (Path where to access stacks; default=current directory)\
+[-v/--verbose]
 ```
 
-- Run a workflow in galaxy: 
+- Run a workflow in galaxy (example): 
  
 ```bash
-$ python3 /path/to/repo/run_workflow_phaeoexplorer.py input_file.yml -c/--config config_file --workflow workflow_type [-v/--verbose] [OPTIONS]
-		--workflow (Valid options: "chado_load_fasta_gff_jbrowse", "blast", "interpro", preset workflows are available in the "workflows_phaeoexplorer" directory)
-		--main-directory $PATH (Path where to access stacks; default=current directory)
+$ python3 /path/to/repo/gga_run_workflow_phaeo_jbrowse.py input_file.yml \
+-c/--config config_file	\
+--main-directory $PATH (Path where to access stacks; default=current directory) \
+[-v/--verbose]
 ```
 
 The data loading into Galaxy with `gga_load_data.py` should be run only once the Galaxy service deployed with `gga_init.py` is ready.