xenome ouput fastq.gz format

[wenkui123]

hi,
Can "xenome classify" output the fastq.gz file directly?

[ghost]

My experience: This tool does not like .gz files.
You could write a script: pipe the output to zip (and delete the unzipped files before it moves to another sample, if multi sample).

[RamRS]

@Himalayan-Java That is not a viable solution, you cannot pipe the output from the tool as it does not write to a pipe-able stream. Like you say though, a script will be useful. I have a xenome classify followed by a bunch of pigzs wrapped in a snakemake rule.