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HRGV / phyloFlash

phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
GNU General Public License v3.0
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phyloFlash.pl: -nozip not functioning #180

Open nick-youngblut opened 1 year ago

nick-youngblut commented 1 year ago

I'm using phyloflash=3.4.2, and running phyloFlash.pl -nozip still results in compressed output. Regardless of -zip or -nozip (or nothing) is used, the output is always compressed

kbseah commented 1 year ago

What was the command you used? The -almosteverything and -everything flags override -nozip.

nick-youngblut commented 1 year ago

I used -almosteverything. Can you point me to the docs that explain how -almosteverything and -everything override -nozip? I missed that when reading the docs.

Why tie the functionality of -nozip with -almosteverything and -everything?

kbseah commented 1 year ago

-zip was implemented first as optional, then switched on by default, before being bundled into options -everything and -almosteverything