Updated test data paths batch 9

[GallVp]

PR checklist

Closes #XXX

• Updated test data paths batch 9
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the module conventions in the contribution docs
• If necessary, include test data in your PR.
• Remove all TODO statements.
• Emit the versions.yml file.
• Follow the naming conventions.
• Follow the parameters requirements.
• Follow the input/output options guidelines.
• Add a resource label
• Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda
  • For subworkflows:
    • nf-core subworkflows test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows test <SUBWORKFLOW> --profile conda

[GallVp]

This issue with nf-test (modules/nf-core/centrifuge/centrifuge, docker_self_hosted) might be solved by using chmod. A similar issue was seen in the past with fastk.

modules/modules/nf-core/fastk/fastk/main.nf

Line 36 in 9a8bba5

find . -name '*.ktab*' \\

I think this is unique to docker_self_hosted due to absence of -u $(id -u):$(id -g) which is because of its own reasons. Any input on this one @mirpedrol ?

modules/tests/config/nf-test.config

Lines 33 to 38 in 9a8bba5

	docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
	}
	docker_self_hosted {
	docker.enabled = true
	docker.fixOwnership = true
	docker.runOptions = '--platform=linux/amd64'

[GallVp]

I'll try to fix the untar in a separate PR.

[GallVp]

It is related to #5970

[GallVp]

Leaving the centrifuge out for now.