update readme part 5

README.md

@@ -49,9 +49,9 @@ wget https://raw.githubusercontent.com/NBISweden/EGA-SE-user-docs/main/crypt4gh_
 wget https://raw.githubusercontent.com/NBISweden/EGA-SE-user-docs/main/crypt4gh_bp_key.pub
 ```
 
-### Encrypt file(s)
+### Encrypt files
 
-After downloading the public key file, you can encrypt your file(s) using the
+After downloading the public key file, you can encrypt your files using the
 `sda-cli` executable obtained in the first step of this guide. To encrypt a
 specific file, use the following command:
 
@@ -75,7 +75,7 @@ command like this:
 ./sda-cli encrypt -key <public_key_file> -continue=true <file_1_to_encrypt> <file_2_to_encrypt>
 ```
 
-### Encrypt file(s) with multiple keys
+### Encrypt files with multiple keys
 
 You can encrypt files using multiple public keys by specifying the `-key` flag
 multiple times. For example:
@@ -136,9 +136,9 @@ ways, listed in order of priority:
 2. From the `ACCESSTOKEN` environment variable.
 3. In the configuration file.
 
-### Upload file(s)
+### Upload files
 
-Once the configuration file has been downloaded, file(s) can be uploaded to the
+Once the configuration file has been downloaded, files can be uploaded to the
 archive using the `sda-cli` executable. To upload a specific file, use the
 following command:
 
@@ -163,7 +163,7 @@ separated by spaces, as shown below:
 - If the input contains unencrypted files, the process will exit early. To
 override this behavior, use the `-force-unencrypted` flag.
 
-### Upload folder(s)
+### Upload folders
 
 You can upload entire directories recursively, including all contained files and
 subfolders while preserving the local folder structure. This can be done using
@@ -205,7 +205,7 @@ The `<upload_folder>` argument can also include a folder path, such as
 to `folder1/folder2/<encrypted_file_1_to_upload>`.
 
 **Note**: To include all the contents of a directory without the directory
-*itself, you can use `/.`. For instance:
+itself, you can append `/.` to `<folder_to_upload>`. For instance:
 
 ```bash
 ./sda-cli -config <configuration_file> upload -r <folder_to_upload>/. -targetDir <new_folder_name>
@@ -243,7 +243,7 @@ the folder recursively (including only the resulting `.c4gh` files) under
 
 - The command internally calls the [encrypt](#Encrypt) module when performing
 encrypt-on-upload, mirroring its behavior, including the creation of hash files.
-- For encryption with [multiple public keys](#Encrypt-file(s)-with-multiple-keys),
+- For encryption with [multiple public keys](#Encrypt-files-with-multiple-keys),
 concatenate all public keys into a single file and provide it using the
 `-encrypt-with-key` flag.
 - If the input includes already encrypted files, the process will exit without
@@ -310,9 +310,9 @@ Depending on the setup of the SDA/BP services, files can be downloaded
 unencrypted or encrypted.
 
 If the service is configured for encrypted downloads, you can download files
-encrypted on the server-side by providing a [public key file](#create-key) using
-the `-pubkey` flag. For detailed instructions, refer to [download encrypted
-files](#download-encrypted-files).
+encrypted on the server-side by providing a
+[public key file](#create-crypt4gh-key-pair) using the `-pubkey` flag. For
+detailed instructions, refer to [download encrypted files](#download-encrypted-files).
 
 The following options are available for downloading files: