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data61 / gossamer

Gossamer bioinformatics suite
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xenome ouput fastq.gz format #31

Open wenkui123 opened 3 years ago

wenkui123 commented 3 years ago

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

ghost commented 2 years ago

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 commented 2 years ago

@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.