Option to set the output directory

[mbhall88]

As the title suggests, it would be great to have an option to designate an output directory rather than using the current directory.

[wwood]

I agree - I'll try to find the time, but PRs welcome.

[mbhall88]

I went to try and work on adding this but there is a lot of assumptions throughout the code that the files will be in the current working directory. I'll leave it to you to decide how the code could be refactored to make this change easier.

[wwood]

Hey,

Yeh - not fun to fix. Luckily today I'm sick so needed something brainless to do. Would you mind testing it out please? There's a bunch of new unit tests but would still benefit from a sanity check from a non-sick-me human.

Thanks.

[mbhall88]

Hi @wwood,

Thanks for getting around to this. Sorry to hear you're sick!

I just tested out the tip of master and the option didn't seem to work.

./bin/kingfisher get --output-directory test-out -r ERR3239713 -m ena-ftp

it created the output directory okay, but still downloaded the fastqs to the current directory.

[wwood]

Ah right, forgot about ENA. Fixed now? For testing you might like to use SRR12118866 instead since it is only 20MB.

[mbhall88]

That seems to have fixed my example! Thanks!