Add pipeline nf-test tests

[mirpedrol]

Description of feature

This issue is to collect all steps to implement pipeline level nf-tests to nf-core pipelines

Tasks

Beta Give feedback

1. Add pipeline level nf-test documentation website#2536
   +0
2. Add pipeline level nf-tests for template #2992
   +0
3. Add nf-test to pipeline template CI workflow #2881
   +0
4. Add linting for pipeline nf-tests (included in Add pipeline level nf-tests for template #2992)
5. Add an option to opt-out nf-tests when creating a custom (non nf-core) pipeline
6. Make sure that all references to old tests are updated (i.e. running pipeline tests with nextflow run)
7. Lint for pipeline nf-test contents #3065
   enhancement +1
8. Lint for tests/nextflow.config contents #3064
   enhancement +1
9. Lint contents of nf-test.config #3063
   enhancement +1
10. linting for nf-test snapshot #3049
    enhancement +1