update README about how to download files

README.md

@@ -88,8 +88,40 @@ curl -s -H "Authorization: Bearer $token" "http://localhost:8443/metadata/datase
 
 ### Download a specific file
 
-```shell
-fileID=$(curl -s -H "Authorization: Bearer $token" "http://localhost:8443/metadata/datasets/$datasetID/files" | jq -r '.[0].fileId')
-filename=$(curl -s -H "Authorization: Bearer $token" "http://localhost:8443/metadata/datasets/$datasetID/files" | jq -r '.[0].displayFileName' | cut -d '.' -f 1,2 )
+The `sda-download` service offers multiple methods for downloading files through the API, with options for both encrypted and unencrypted results. Below, you will find an example illustrating each of these methods.
+
+First,  obtain the `fileID` and `filename` using the following command. The `datasetID`, which is `DATASET0001`, can be obtained by following the instructions at [List datasets](#list-datasets)
+
+```bash
+fileID=$(curl -s -H "Authorization: Bearer $token" "http://localhost:8443/metadata/datasets/$datasetID/files" | jq -r '.[1].fileId')
+filename=$(curl -s -H "Authorization: Bearer $token" "http://localhost:8443/metadata/datasets/$datasetID/files" | jq -r --arg fileID "$fileID" '.[] | select(.fileId == $fileID) | .displayFileName | rtrimstr(".c4gh")')
+```
+
+#### 1. Download unencrypted file from the `/files` endpoint
+```bash
 curl -s -H "Authorization: Bearer $token" http://localhost:8443/files/$fileID -o "$filename"
 ```
+After successful execution, the BAM file `htsnexus_test_NA12878.bam` will be downloaded to your current folder.
+
+#### 2. Download unencrypted file from the `/s3` endpoint
+```bash
+curl -s -H "Authorization: Bearer $token" http://localhost:8443/s3/$datasetID/$filename -o "$filename"
+```
+
+#### 3. Download encrypted file from the `/s3-encrypted` endpoint
+To download an encrypted file that is re-encrypted with a custom Crypt4GH public key, you need to first create a key pair by the [`sda-cli`](https://github.com/NBISweden/sda-cli) tool, instructions can be found [here](https://github.com/NBISweden/sda-cli?tab=readme-ov-file#create-keys).
+
+```bash
+# create a crypt4gh key pair
+sda-cli createKey c4gh
+```
+```bash
+pubkey=$(base64 -w0 c4gh.pub.pem) 
+curl -s -H "Authorization: Bearer $token" -H "Client-Public-Key: $pubkey" http://localhost:8443/s3-encrypted/$datasetID/$filename -o "$filename.c4gh"
+```
+
+After successful execution, the Crypt4GH encrypted BAM file `htsnexus_test_NA12878.bam.c4gh` will be downloaded to your current folder. This file can be decrypted using the private key of the key pair you have created by
+
+```bash
+sda-cli decrypt -key c4gh.sec.pem htsnexus_test_NA12878.bam.c4gh
+```