Scripts should be converted to use a single config file to obtain arguments for executing the script rather than accepting parameters from the command line. For example, get_sequence_ids.pl takes an argument --families ..., and this should be instead inserted into a JSON configuration file. The reason for this change is to enhance security by preventing external input from being executed on the command line inside of pipelines (for example, if the input to --families comes from a web form, and malicious data was inserted, that could be executed by the pipeline script). @rbdavid
Scripts should be converted to use a single config file to obtain arguments for executing the script rather than accepting parameters from the command line. For example,
get_sequence_ids.pltakes an argument--families ..., and this should be instead inserted into a JSON configuration file. The reason for this change is to enhance security by preventing external input from being executed on the command line inside of pipelines (for example, if the input to--familiescomes from a web form, and malicious data was inserted, that could be executed by the pipeline script). @rbdavid