Compressed output if input is compressed

[andersgs]

Hello. Thank you for goalign.

It is great that goalign will take compressed input. But, I noticed that the output is not compressed. Would it be possible for the output to mirror the input compression? For instance, if the input is gzipped the output be also gzipped. Perhaps as a flag option to enable output compression, giving the user the option to compress the output if they wish.

Thanks again.

[fredericlemoine]

Hello,

Thank you for your suggestion. I added the possibility to output gz and xz compressed files, if they have .gz or .xz extension.
For example:

goalign reformat phylip -i a.fasta -o a.phylip.gz

Should produce a gz compressed file.

I prefer the output compression to be independent of the input compression, allowing more flexibility.
I may create a new release in the coming days, but feel free to test it in the meantime.

[andersgs]

Thank you @fredericlemoine. I will give it a go. A new release would be great. And, yes, I agree that giving the user the choice of compressing the output would be ideal.

[andersgs]

Just FYI @fredericlemoine I am adding modules to nf-core for goalign.

[fredericlemoine]

Good to know, thanks. Is this this PR? nf-core/modules#1785 ?

[andersgs]

Yes. That is the first one. I'll add one per sub-command. Once the first one is done, it should be trivial to add the others.

[fredericlemoine]

Great, thanks. Let me know if you need help at some point.
I close this issue.