Updated Nextstrain's docs

docs/markdown_files/howto_nextstrain.md

@@ -1,6 +1,6 @@
 # How to use Nextstrain
 
-After you have correctly installed **Nextstrain** by following the steps described in the [README](https://github.com/Shettland/relecov-platform/tree/develop#install-nextstrain), you need to prepare your data and configuration files to run Nextstrain.
+After you have correctly installed **Nextstrain** by following the steps described in the [README](https://github.com/BU-ISCIII/relecov-platform/blob/main/README.md), you need to prepare your data and configuration files to run Nextstrain.
 
 Once Nextstrain is installed, clone the repository https://github.com/BU-ISCIII/nexstrain_relecov.git and copy it into the `datasets/sars-cov-2/` directory. For clarity, we will refer to this copy as the "build_folder."
 
@@ -20,10 +20,10 @@ ccggaggattccggattgtcaatatgcccggaggattccggattgtcaatatgcccggaa
 
 The header of the metadata table may vary depending on the metadata that you want to use, but you can find a reference [here](https://github.com/BU-ISCIII/nexstrain_relecov/blob/master/data/example_metadata.tsv). 
 
-For a basic analysis, not all the headers are necessary. The relecov's custom script [metadata_nextstrain_parser.py](https://github.com/BU-ISCIII/nexstrain_relecov/tree/master/data) can be run to parse the metadata processed with the `relecov-tools` from JSON format to TSV format:
+For a basic analysis, not all the headers are necessary. The relecov's custom script [metadata_nextstrain_parser.py](https://github.com/BU-ISCIII/relecov-tools/blob/main/relecov_tools/assets/pipeline_utils/metadata_nextstrain_parser.py) can be run to parse the metadata processed with the `relecov-tools` from JSON format to TSV format, by taking all JSON files stored within a specific directory, as shown in the following command:
 
 ```
-python metadata_nextstrain_parser.py relecov_metadata.json relecov_metadata.tsv
+python3 metadata_nextstrain_parser.py --input-dir json_files/
 ```
 
 The next step would be to customize the config file `relecov_data.yaml` to your needs. You may find information on how to do this task [here](https://docs.nextstrain.org/projects/ncov/en/latest/reference/workflow-config-file.html).

docs/markdown_files/nextstrain_install.md

@@ -48,12 +48,12 @@ cp -r /path/to/auspice /opt/nextstrain/dataset/sars-cov-2
 The service configuration file is located in the **conf** directory of the relecov-platform.
 If you change the installation folder from `/opt` to a different location, replace 
 `/opt/` for your installation folder.
-Copy the service file to `/usr/lib/systemd/system`
+Copy the service file to `/etc/systemd/system`
 ```
-sudo cp /opt/relecov-platform/conf/nextstrain.service /usr/lib/systemd/system
+sudo cp /opt/relecov-platform/conf/nextstrain.service /etc/systemd/system
 ```
 By default, the service listens on port 8100. If you need to change this port, 
-edit `/usr/lib/systemd/system` and replace the default port number with your desired value, then save the file.
+edit `/etc/systemd/system` and replace the default port number with your desired value, then save the file.
 
 ### Start Nexstrain service
 To get the service up, you need to start the service: