A question on linting: In my last PR, the linting step fails because the snapshot has a md5sum of an empty file. Why is this an issue? Shouldn't this be expected for each file that is created in stub mode?

Is the stub test named with " - stub" at the end?

Yes:

"homo_sapiens - [ bam, bai ], [] - stub"

Also, I haven't touched this test in my PR, I only added a new one (I then used

--clean-snapshot --update-snapshot

to update the snapshot before submitting it as part of the PR).

Probably the issue is with one of the other tests.

"homo_sapiens - [ bam, bai ], config - stub - csi_index"

doesn't have

stub

at the end, so might be that. Or it could be in

"homo_sapiens - [ bam, bai ], no_vcf"

, which has the

d41d8cd98f00b204e9800998ecf8427e

string as the output of

bam(process.out.bam.get(0).get(1)).getReadsMD5()

inside the test. Could you swap the module to use a topic for the versions as well, while you are modifying it?

Thanks, Simon. I'm new to this and have some follow-up questions: • how can I run these linting steps locally, only against the module, to check if something's wrong upfront? • what do you mean by swapping modules? • what do you mean by using a topic? (do you refer to the

-

interleaved strings in the test description?)

ad 1)

nfcore modules lint $module_name

(or even without

$module_name

where you get a selection field then) ad 2) https://deploy-preview-3612--nf-core-docs.netlify.app/docs/tutorials/migrate_to_topics/update_modules

Thanks, Matthias. I'll have a read later! 🙂

Yeah, basically we are in the midst of changing over all the ~1700 modules in the repository, so if you are able to do this one while you are updating it anyway that'd be great

Thanks, Simon!

Just shout if you need further help