Cannot sort Channel

[maxulysse]

Hej,

I'm seeing this warning, while trying to make a test at the workflow level, any idea on how to deal with it?

Warning: Cannot sort channel, order not deterministic. Unsupported objects types: class org.apache.groovy.json.internal.LazyMap vs. class org.apache.groovy.json.internal.LazyMap

[lukfor]

Thanks for reporting this. do you have an example at hand or a link to the test file?

[maxulysse]

yes, I'm currently trying to use nf-test to assess workflows in the fetchngs pipeline cf nf-core/fetchngs#191

[lukfor]

Thanks! I will look into this. I think it depends on the nested elements of the output channel.

I noticed you disabled autoSort in nf-test.config for all testcases. If you add for exampple process.out to a snapshot, this could lead to failed tests, because the order of elements is not deterministic without sorting. Thus, the order in the snapshot could be different as the order of the current test run.

[maxulysse]

Yeah, I disabled autoSort to get rid of the warning.
Since it couldn't sort, the workflow.out snapshot were failing anyway, so I'm currently just looking at the files.

[maxulysse]

made a more tiny reproducible example: https://github.com/maxulysse/nf-test_109

[lukfor]

Thanks, this helps us a lot! 🙌

A first try with this fix seems to solve the auto-sort problem.But I will check it again tomorrow 👍

However, I noticed that the zip files (e.g. test_pair_1_fastqc.zip) have a different md5 on each run. Thus, the snapshot matching failes :/

[maxulysse]

yeah, but no worries about that, my plan was to catch the snapshot of the versions, not the zip.

[lukfor]

PR #115 should fix this issues. Same here, I'm leaving the issue open until we create a new release and you confirm its resolution.

[lukfor]

We have just released RC1 of version 0.8.0 🎉
This is a pre-release and can be installed using the following command:

curl -fsSL https://code.askimed.com/install/nf-test | bash -s 0.8.0-rc1

If everything works as expected, please feel free to close this issue. Thanks for your support! 🙏

[adamrtalbot]

I'm still seeing this problem on v0.8.0 rc1 when I'm using a channel of 1 file with the same name (versions.yml and different md5 values:

https://github.com/nf-core/modules/actions/runs/6147043260/job/16677642592?pr=3809

[lukfor]

Thank you for testing! 👍 Did you recreate the snapshots with v0.8.0 rc1? Since nf-test < 0.8.0 created unsorted snapshots.

[adamrtalbot]

Yep - interestingly the test runs fine on my laptop (Mac) but not the Github Action runner.

[lukfor]

Thanks 👍 I will look at it in detail

[adamrtalbot]

Thank you!

Related PR: nf-core/modules#3809

[maxulysse]

Still having the issue as well: nf-core/fetchngs#192

[drpatelh]

Hola @lukfor ! We are trying to finalise our nf-test implementation in the nf-core/fetchngs pipeline before the Hackathon and this is the only remaining issue (for now) that we would love to see fixed and in a release. Would you have any timeline for when you can squeeze this in? Thank you!

[lukfor]

Hi guys, I was unfortunately very busy the last few weeks 🤯 I'll see that I have a release ready by the beginning of next week. Maybe I will find some time on the weekend 🚀

[lukfor]

I have just built 0.8.0-rc2. You can install it as follows:

curl -fsSL https://code.askimed.com/install/nf-test | bash -s 0.8.0-rc2

The snapshots have to be recreated and then it should now work with the versions channel.

If this fixes your issues, I will build and release 0.8.0 👍

[maxulysse]

I'll test it right away

[maxulysse]

looking good for me: nf-core/fetchngs#201