diff --git a/src/interface/parse_args.hpp b/src/interface/parse_args.hpp index 4621bae7..d9996082 100644 --- a/src/interface/parse_args.hpp +++ b/src/interface/parse_args.hpp @@ -67,8 +67,8 @@ void parse_args(int argc, parser.helpParams.eachgroupindent = 2; args::Group options_group(parser, ""); - args::Positional target_sequence_file(options_group, "target.fa", "input target FASTA file"); - args::Positional query_sequence_file(options_group, "query.fa", "input query FASTA file (optional: if not given, target.fa will be used as query)"); + args::Positional target_sequence_file(options_group, "target.fa", "target sequences (required)"); + args::Positional query_sequence_file(options_group, "query.fa", "query sequences (optional, defaults to target)"); args::Group indexing_opts(options_group, "Indexing:"); args::ValueFlag write_index(indexing_opts, "FILE", "build and save index to FILE", {'W', "write-index"}); args::ValueFlag mashmap_index(indexing_opts, "FILE", "use pre-built index from FILE", {'i', "index"});