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71	71	In another browser tab, open [[https:~~/~~/lab.ebrains.eu>>https://lab.ebrains.eu]]
72	72
73	73	* **Edit the config files**
74		-Each stage has a config file (//pipeline/<stage_name>/config.yaml//) to specify which analysis/processing blocks to execute and which parameters to use. General and specific information about the blocks and parameters can be found in the README and config files of each stage. The default values are set for an example dataset (ECoG, anesthetized mouse, [[IDIBAPS>>https://kg.ebrains.eu/search/?facet_type[0]=Dataset&q=sanchez-vives#Dataset/2ead029b-bba5-4611-b957-bb6feb631396]]]).
	74	+Each stage has config files (//pipeline/<stage_name>/configs/config_<profile>.yaml//) to specify which analysis/processing blocks to execute and which parameters to use. General and specific information about the blocks and parameters can be found in the README and config files of each stage. There are preset configuration profiles for the benchmark datasets IDIBAPS ([[ECoG, anesthetized mouse>>https://kg.ebrains.eu/search/?facet_type[0]=Dataset&q=sanchez-vives#Dataset/2ead029b-bba5-4611-b957-bb6feb631396]]) and LENS ([[Calcium Imaging, anesthetized mouse>>https://kg.ebrains.eu/search/instances/Dataset/71285966-8381-48f7-bd4d-f7a66afa9d79]]).
75	75
76	76	* **Run the notebook**
77	77	In the jupyter hub, navigate to //drive/My Libraries/My Library/pipeline/showcase_notebooks/run_snakemake_in_collab.ipynb//, or where you copied the //pipeline// folder to.
...	...	@@ -85,12 +85,13 @@
85	85	=== ii) Local execution ===
86	86
87	87	* **Get the code**
88		-The source code of the pipeline is available via Github: [[INM-6/wavescalephant>>https://github.com/INM-6/wavescalephant]] and can be cloned to your machine ([[how to Github>>https://guides.github.com/activities/hello-world/]]).
	88	+The source code of the pipeline is available via Github: [[INM-6/wavescalephant>>https://github.com/INM-6/wavescalephant]] and can be cloned to your machine ([[how to get started with Github>>https://guides.github.com/activities/hello-world/]]).
89	89
90	90	* (((
91	91	**Build the Python environment**
92		-In the wavescalephant git repository, there is an environment file ([[pipeline/envs/wavescalephant_env.yml>>https://drive.ebrains.eu/lib/905d7321-a16b-4147-8cca-31d710d1f946/file/pipeline/envs/wavescalephant_env.yml]]) specifying the required packages and versions. To build the environment, we recommend using conda ([[how to get started with conda>>https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html]]).
93		-##conda env create ~-~-file /envs/wavescalephant_env.yml##
	92	+In the wavescalephant git repository, there is an environment file ([[pipeline/environment.yaml>>https://drive.ebrains.eu/smart-link/1a0b15bb-be87-46ee-b838-4734bc320d20/]]) specifying the required packages and versions. To build the environment, we recommend using conda ([[how to get started with conda>>https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html]]).
	93	+##conda env create ~-~-file environment.yaml
	94	+conda activate wavescalephant_env##
94	94
95	95	)))
96	96	* **Edit the settings**
...	...	@@ -97,14 +97,14 @@
97	97	The settings file specifies the path to the output folder, where results are saved to. Open the template file //[[pipeline/settings_template.py>>https://drive.ebrains.eu/lib/905d7321-a16b-4147-8cca-31d710d1f946/file/pipeline/settings_template.py]]//, set the ##output_path## to the desired path, and save it as //pipeline/settings.py//.
98	98
99	99	* **Edit the config files**
100		-Each stage has a config file to specify which analysis/processing blocks to execute and which parameters to use. Edit the config template files //pipeline/stageXX_<stage_name>/config_template.yaml// according to your dataset and analysis goal, and save them as //pipeline/stageXX_<stage_name>/config.yaml//. A detailed description of the available parameter settings and their meaning is commented in the template files, and a more general description of the working mechanism of each stage can be found in the respective README file //pipeline/stageXX_<stage_name>/README.md//.
	101	+Each stage uses a config file to specify which analysis/processing blocks to execute and which parameters to use. Edit the config template files //pipeline/stageXX_<stage_name>/configs/config_template.yaml// according to your dataset and analysis goal, and save them as //pipeline/stageXX_<stage_name>/configs/config_<profile>.yaml//. A detailed description of the available parameter settings and their meaning is commented in the template files, and a more general description of the working mechanism of each stage can be found in the respective README file //pipeline/stageXX_<stage_name>/README.md//.
101	101	//Links are view-only//
102	102	** full pipeline: [[README.md>>https://drive.ebrains.eu/smart-link/d2e93a2a-09f6-4dce-982d-0370953a4da8/]], [[config.yaml>>https://drive.ebrains.eu/smart-link/7948fbb3-bf8a-4785-9b28-d5c15a1aafa7/]]
103		-** stage01_data_entry: [[README.md>>https://drive.ebrains.eu/smart-link/896f8880-a7d1-4a30-adbf-98759860fed5/]], [[config.yaml>>https://drive.ebrains.eu/smart-link/d429639d-b76e-4093-8fad-a25463d41edc/]]
104		-** stage02_processing: [[README.md>>https://drive.ebrains.eu/smart-link/01f21fa5-94f7-4883-8388-cc50957f9c81/]], [[config.yaml>>https://drive.ebrains.eu/f/b1607671f6f2468ahttps://drive.ebrains.eu/smart-link/02a3f92c-dc7d-4b33-94f5-91b00db060d5/a43c/]]
105		-** stage03_trigger_detection: [[README.md>>https://drive.ebrains.eu/smart-link/18d276cd-a691-4ee1-81c6-7978cef9c1b4/]], [[config.yaml>>https://drive.ebrains.eu/smart-link/76adbb12-7cb4-42df-9fd5-735927ea3ba8/]]
106		-** stage04_wavefront_detection: [[README.md>>https://drive.ebrains.eu/smart-link/a8e80096-06a0-4ff4-b645-90e134e46ac5/]], [[config.yaml>>https://drive.ebrains.eu/smart-link/6b0b233f-30b7-4bbd-8564-1abebd27ea6d/]]
107		-** stage05_wave_characterization: [[README.md>>https://drive.ebrains.eu/smart-link/3009a214-a11f-424c-8a6e-13e7506545eb/]], [[config.yaml>>https://drive.ebrains.eu/smart-link/471001d5-33f5-488e-a9a4-f03b190e3da7/]]
	104	+** stage01_data_entry: [[README.md>>https://drive.ebrains.eu/smart-link/896f8880-a7d1-4a30-adbf-98759860fed5/]], [[config.yaml>>https://drive.ebrains.eu/smart-link/9bef8f59-1007-48c4-b5ba-30de4ff18f34/]]
	105	+** stage02_processing: [[README.md>>https://drive.ebrains.eu/smart-link/01f21fa5-94f7-4883-8388-cc50957f9c81/]], [[config.yaml>>https://drive.ebrains.eu/smart-link/7e75caf6-e2d6-4393-a97c-4f481c908cf8/]]
	106	+** stage03_trigger_detection: [[README.md>>https://drive.ebrains.eu/smart-link/18d276cd-a691-4ee1-81c6-7978cef9c1b4/]], [[config.yaml>>https://drive.ebrains.eu/smart-link/dfa375c0-cc80-4f95-b3ed-40140acbd96b/]]
	107	+** stage04_wavefront_detection: [[README.md>>https://drive.ebrains.eu/smart-link/a8e80096-06a0-4ff4-b645-90e134e46ac5/]], [[config.yaml>>https://drive.ebrains.eu/smart-link/3a54be8c-b9f4-4698-a85d-6ad97990b40a/]]
	108	+** stage05_wave_characterization: [[README.md>>https://drive.ebrains.eu/smart-link/3009a214-a11f-424c-8a6e-13e7506545eb/]], [[config.yaml>>https://drive.ebrains.eu/smart-link/83f68955-0ca8-4123-9734-6e93349ca3e3/]]
108	108
109	109	* **Enter a dataset**
110	110	There are two test datasets in the collab drive (IDIBAPS and LENS) for which there are also corresponding config files and scripts in the data_entry stage. So, these datasets are ready to be used and analyzed.
...	...	@@ -111,8 +111,8 @@
111	111	For adding new datasets see //[[pipeline/stage01_data_entry/README.md>>https://drive.ebrains.eu/smart-link/d2e93a2a-09f6-4dce-982d-0370953a4da8/]]//
112	112
113	113	* **Run the pipeline (-stages)**
114		-To run the pipeline with [[snakemake>>https://snakemake.readthedocs.io/en/stable/]]), activate the Python environment ##conda activate wavescalephant_env,## make sure you are in the working directory (pipeline/), and call ##snakemake## to run the entire pipeline.
115		-To (re-)execute an individual stage, you can navigate to the corresponding stage folder and call the ##snakemake## command there. For running an individual stage, you may need to manually set the path for input file for the stage (i.e. the output file of the previous stage) in the config file ##INPUT: /path/to/file##.
	115	+To run the pipeline with [[snakemake>>https://snakemake.readthedocs.io/en/stable/]]), activate the Python environment ##conda activate wavescalephant_env,## make sure you are in the working directory (//pipeline/)//, and call ##snakemake## to run the entire pipeline.
	116	+For a more detailed executed guide and how to execute individual stages and blocks see the pipeline [[Readme>>https://drive.ebrains.eu/smart-link/3009a214-a11f-424c-8a6e-13e7506545eb/]].
116	116
117	117	== Accessing and using the results ==
118	118