search

zjshi / gt-pro

MIT License
23 stars 7 forks source link

%{in} not using just base name #36

Closed nick-youngblut closed 3 years ago

nick-youngblut commented 4 years ago

The gt_pro help docs state:

%{in} expands to the corresponding input base name

...but the base name is not used. Instead the entire input file path is used. For instance, if I provide -o /path/to/gt-pro/output/%{in} /path/to/input/reads.fq, then the output is written to /path/to/gt-pro/output/path_to_input_reads.tsv. In other words, gt_pro is using the entire input file path for %{in} and just converting the / characters to _, instead of just using the basename (eg., reads.fq).

zjshi commented 3 years ago

Yes, this can be achieved using the -C flag. Let me know please if you have any issues getting it work.