%{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).
The
gt_pro
help docs state:...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
).