-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>-trimmedinstead, 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