A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Anyone around for a review of a subworkflow update to try and address the symlinking issue with Kraken?

<https://github.com/nf-core/createtaxdb/pull/115>

<@UEM37TBAR> I'm on phone right now and can't quickly check. Does the subworkflow test now cover the case of local files or not? The changes only included the snapshots.

No, doesn't test local files :disappointed:

The one I reported back, or you mean our CI tests/

The tests corresponding to subworkflows/nf-core/fasta_build_add_kraken2_bracken/main.nf

The tests for that were run on Github actions which only uses URLs, but when I test the updated subworkflow in the pipeline  with local files running on my laptop it works (well, Bracken breaks, but that's a spearate issue)

Is it a separate issue? Your comment indicates it is related? But good to know you confirmed it. I might be able to take a better look tonight. And I think having a test scenario for local files would be good to have.

It's the same issue, just in the next module along the chain. I'm expect the same issue with `tar` too

Yeah, I agree it would be good to have, but I'm not sure how we can get that scccccnario to run on github actions

Download all files prior :grimacing: I can investigate

Yeah I meant more will we break something for the nf-testing stuff - it'll be potentially a lot more than just download all files prior (making new samplesheets etc)

(which is why I've not done it yet :sweat_smile: )

Ah right yeah, the reason why we missed `tar` before too, is because the 'keep intermediates' flag (which would include  the local files) is run in the test that doesn't do tarring.

If I run `test` on my PR skip bracken, but turn on `--kraken2_keepintermediates` then it crashes with the same 'can't find &lt;local&gt; files' error

Does nextflow use absolute or relative symlinks? Does moving them break them?