xenome ouput fastq.gz format

Question

xenome ouput fastq.gz format

wenkui123 opened this issue 3 years ago · comments

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

Himalayan_Java · Answer 1 · Tue Jun 07 2022 04:08:39 GMT+0800 (China Standard Time)

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).

Ram Srinivasan · Answer 2 · Sat Jul 09 2022 04:24:40 GMT+0800 (China Standard Time)

@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.