Hi! I'm currently working on a PR for the pipeline and I had issues for updating the snapshots of the pipeline tests following the recommended workflows (input errors and obviously incorrect snapshot). I did manage to find that running the tests required

--profile=+test,singularity

instead of

--profile=+singularity

and someone pointed out that the pipeline used a slightly different config that the rest. rnaseq (no profile test provided):

// run all tests with the profile(s) specified by each CI workflow

other:

// run all test with defined profile(s) from the main nextflow.config
profile "test"

Is this an intended behaviour ? If so can we add a note somewhere for future contributors ?

Yes, this is intentional! The rnaseq pipeline deliberately doesn't set

profile "test"

in

nf-test.config

because it needs to support both CPU and GPU test profiles. The pipeline has two CI workflows: one for CPU tests that passes

--profile=+test,docker

(or singularity/conda), and a separate GPU workflow that passes

--profile=+test_gpu,docker

. The

test

and

test_gpu

profiles have different resource limits (15 GB vs 30 GB), and if

profile "test"

were hardcoded in

nf-test.config

, the GPU workflow wouldn't be able to override it with

test_gpu

(due to how Nextflow profile config precedence works). So when running tests locally, you do need to include the

test

profile explicitly, e.g.

nf-test test --profile=+test,singularity

. That's a fair point about adding a note for contributors though - I'll look into adding something to the contributing docs or a comment in

nf-test.config

to make this clearer.

Ok thanks for the explanation !