-o, --output <str> Base name of output file; ('<reads>.trimmed')
However, the output files instead are prefixed by <str>-trimmed instead, followed by .<ext> for the fastq(.gz) and log files. That is, the help message should replace <reads> by <str>, and the . dot by a - dash.
This is just a minor issue, but still caused confusion, as I am trying to write a Snakemake pipeline that relies on specific file names.
Hi there!
The help states:
However, the output files instead are prefixed by
<str>-trimmed
instead, followed by.<ext>
for the fastq(.gz) and log files. That is, the help message should replace<reads>
by<str>
, and the.
dot by a-
dash.This is just a minor issue, but still caused confusion, as I am trying to write a Snakemake pipeline that relies on specific file names.
Thanks Lucas