'run.sh' Script Fails Due to Missing Input Arguments

[astoicame]

Describe the bug

The bash script run.sh fails to execute pipeline initiation due missing input arguments. The script fails to take the required input projectID, producing a housekeeping message which states: All variables are required: profile outDir projectID. Even once this is provided, the script also fails to ask for the --input argument required for the Nextflow command, producing an error message which states: 'ERROR ~ ERROR: Validation of pipeline parameters failed! * Missing required parameter: --input.

To Reproduce

For the initial error run the command to execute run.sh in the project directory:

bash run.sh <profile> <outDir> <projectID> 

Once projectID=$3 has been added to the input parameters, run the command again for the --input error.

Expected behavior
This script should ensure all needed arguments are provided, make the results directory specified, and then run the NextFlow pipeline.