Fixed small issues

README.md

@@ -66,7 +66,7 @@ A step by step series of commands that tell you how to setup properly the transf
 Start by cloning the transfer-tool on your local machine:
 
 ```bash
-git clone git@gitlab.sib.swiss:SPSP/transfer-tool.git
+git clone https://gitlab.isb-sib.ch/SPSP/transfer-tool.git
 ```
 
 Then get inside the directory:
@@ -78,9 +78,9 @@ ls -la
 
 Your terminal should output 3 folders (logs,outbox,sent) and 2 files (README.md, spsp) and 2 hidden files (.env, .pub). Here is a short description of each folder and file:
 
-- **logs** - contains all the log files when you use the auto mode (log files record only errors)
-- **outbox** - contains files to be sent to the SPSP server through sftp
 - **sent** - contains encrypted files with their SHA256 hash that have been properly sent
+- **.logs** - contains all the log files when you use the auto mode (log files record only errors)
+- **.outbox** - contains files to be sent to the SPSP server through sftp
 - *README.md* - user guide
 - *spsp* - script containing all the commands to run, type `./spsp help` to display the commands
 - *.env* - setting file to be configured by the user
@@ -99,7 +99,7 @@ This will make sure that some commands are available, that the script is executa
 Next, you need to configure the .env file to use the correct ID. Open the file with a text editor and change the line below:
 
 ```
-ID=labo1 #CHANGE THIS LINE BY USING YOUR OWN ID PROVIDED BY THE SPSP BOARD
+ID=TST_0001 #CHANGE THIS LINE BY USING YOUR OWN ID PROVIDED BY THE SPSP BOARD
 HOST=spsp-sftp.vital-it.ch
 SFTP_URL=${ID}@${HOST}:/data
 ```

spsp

@@ -64,7 +64,7 @@ showHelp() {
     commands="$commands  compress <folder>           Compress the ${COL_LGREEN}FASTQ${COL_RESET} and ${COL_LGREEN}XSLX${COL_RESET} files to ${COL_LYELLOW}tar.gz${COL_RESET} file\n"
     commands="$commands  encrypt <compressed file>   Encrypt a ${COL_LGREEN}tar.gz${COL_RESET} file using a public key\n"
     commands="$commands  transfer <encrypted file>   Transfer the encrypted file using ${COL_LGREEN}SFTP${COL_RESET}\n"
-    commands="$commands  auto                        Automatically run the commands to ${COL_CYAN}Compress${COL_RESET}, ${COL_GREEN}Encrypt${COL_RESET} & ${COL_MAGENTA}Transfer${COL_RESET}\n"
+    commands="$commands  auto                        Automatically run the commands to ${COL_CYAN}Compress${COL_RESET}, ${COL_GREEN}Encrypt${COL_RESET} & ${COL_MAGENTA}Transfer${COL_RESET}, add --no-archive to not save any archive sent\n"
     commands="$commands  help                        Shows Help screen\n"
 
     options="${COL_LYELLOW}Options:\n${COL_RESET}"