Add Eigenstratdatabasetools/snpcoverage

[TCLamnidis]

Add module for eigenstratdatabsetools/snpcoverage.

PR checklist

Closes #853

• [x] This comment contains a description of changes (with reason).
• [x] If you've fixed a bug or added code that should be tested, add tests!
• [x] If you've added a new tool - have you followed the module conventions in the contribution docs
• [x] If necessary, include test data in your PR.
• [x] Remove all TODO statements.
• [x] Emit the versions.yml file.
• [x] Follow the naming conventions.
• [x] Follow the parameters requirements.
• [x] Follow the input/output options guidelines.
• [x] Add a resource label
• [x] 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:
  • [x] PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
  • [ ] PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
  • [x] PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

[TCLamnidis]

PileupCaller module is required to avoid using local test data.

[nvnieuwk]

Hi, you have to upload some test data for GitHub Actions to use as the test samples. You can do this on https://github.com/nf-core/test-datasets/tree/modules on the branch modules. You can then add the data to tests/config/test_data.config. If you then use the samples specified in this config file in tests/modules/eigenstratdatabasetools/coverage/main.nf, your tests should pass :)

[jfy133]

Hi, you have to upload some test data for GitHub Actions to use as the test samples. You can do this on https://github.com/nf-core/test-datasets/tree/modules on the branch modules. You can then add the data to tests/config/test_data.config. If you then use the samples specified in this config file in tests/modules/eigenstratdatabasetools/coverage/main.nf, your tests should pass :)

TYhanks @nvnieuwk ! In this case I think @TCLamnidis doesn't want to pollute test-data with highly specific test data for a single tool, thus his comment of "PileupCaller module is required to avoid using local test data.". I.e. @TCLamnidis will make the upstream module and insert this as a first step in the workflow. Thus we can review it, but I'll switch it to draft for now to make this clear it's not 100% ready.

[nvnieuwk]

Hi, you have to upload some test data for GitHub Actions to use as the test samples. You can do this on https://github.com/nf-core/test-datasets/tree/modules on the branch modules. You can then add the data to tests/config/test_data.config. If you then use the samples specified in this config file in tests/modules/eigenstratdatabasetools/coverage/main.nf, your tests should pass :)

TYhanks @nvnieuwk ! In this case I think @TCLamnidis doesn't want to pollute test-data with highly specific test data for a single tool, thus his comment of "PileupCaller module is required to avoid using local test data.". I.e. @TCLamnidis will make the upstream module and insert this as a first step in the workflow. Thus we can review it, but I'll switch it to draft for now to make this clear it's not 100% ready.

Oh okay, my bad :p

[jfy133]

Hi, you have to upload some test data for GitHub Actions to use as the test samples. You can do this on https://github.com/nf-core/test-datasets/tree/modules on the branch modules. You can then add the data to tests/config/test_data.config. If you then use the samples specified in this config file in tests/modules/eigenstratdatabasetools/coverage/main.nf, your tests should pass :)

TYhanks @nvnieuwk ! In this case I think @TCLamnidis doesn't want to pollute test-data with highly specific test data for a single tool, thus his comment of "PileupCaller module is required to avoid using local test data.". I.e. @TCLamnidis will make the upstream module and insert this as a first step in the workflow. Thus we can review it, but I'll switch it to draft for now to make this clear it's not 100% ready.

Oh okay, my bad :p

No worries! You're technically correct, but in some cases it's not necessary to have explicit test data - the test-data repo is ballooning currently, so if you can just generate the input with very quick preparation steps in the test workflow it's normally worth it!