create-test-yml: move 'work' and '.nextflow*' files to tmp directory

[KevinMenden]

Currently, nf-core modules create-test-yml creates the "work" directory and ".nextflow" files in the current working directly (which is "modules"). These files should be moved to the tmp directory used for creating the output.

[KevinMenden]

Alright I have had another go at this. Essentially there are three things that pollute the CWD, which is the clone of modules:

• work
• .nextflow/
• .nextflow.log

It's possible to direct the .nextflow.log files to the tmp directories by adding a -log directive to the nextflow command before running it. The work and .nextflow/ can't be redirected that way unfortunately, that would require a new workDir directive which can only be modified in an additional config file. However we are already using a custom config file via -c.
So from what I understand the only solution to clean things up would be to manually remove them.
nextflow clean -f doesn't really work either (needs workflow name, doesn't remove the work directory ...).

So this is not super important, I would say we wait until something more elegant from the nextflow side is available, see here for instance:

seqeralabs/nf-tower#279
nextflow-io/nextflow#452

Not sure when this will be available though.

[ewels]

I thought that -w set the work directory from the command line?

[KevinMenden]

😱
Do you happen to have the part in the nextflow documentation that explains that? I've been looking through it for a while but all I could find was the workDir directive and search didn't help .... 😏
I never find stuff on documentation pages.

Well anyway thanks! In that case I guess we could at least direct the work dir and the .nextflow.log to the tmp-dirs. I think the .nextflow/ folder will still exist though, but it's better than nothing.

[ewels]

Yeah these flags can be tricky to find. nextflow help run | grep "-w"? 😅

Not sure about the hidden log dirs, that might be harder as you say..

[ewels]

Found it: https://www.nextflow.io/docs/latest/cli.html#run

[KevinMenden]

Yeah that works if you know what to look for :P also I just looked at the documentation 😏

Okay so the search function on that documentation really doesn't work and I am too dumb to search. Alright I guess we can already start adding that to the code, and then it's only the hidden logs left, which is something we can live with for now I'd say 👍

[drpatelh]

Closed by #1098