Is there some consensus around use of

gzip

vs

bgzip

in modules? I realized that using gzip can be a massive pita when things go to samtools later, since it refuses to take things that are not

bgzip

'ped. Is it preferred to take gzipped module output and un + bgzip again via https://nf-co.re/modules/htslib_bgziptabix/, patch whatever module I use to not gzip and instead pass the output fasta to

htslib_bgziptabix

? Or some better solution (update module + container to use bgzip)?

We've had problems with downstream modules not being able to read

bgzip

stuff

Hm, okay, in that case I think I will patch the module that gzips to not gzip and instead pass the fasta to htslib_bgziptabix

Again: the failure is rare though

Well, if there are failures in both "directions" I am not sure if patching things in the modules repo to facilitate my personal usage is very helpful

Fair opint

I guess it might depend on the expected next steps for the tool

For me specifically it was gfatools, which probably goes into samtools quite often

I think for me it should be prefer bgzip for biological files

Is there a preferred standalone bgzip, or does it always come via htslib?

Pretty certain the best way to get it is htslib

> (I think itwas java with a quite basic gzip reading library or something) There is bgzip support in JVM-based tools, but perhaps not across the board