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Goalign cleanseqs
Closes #1782
PR checklist
- [X] If you've added a new tool - have you followed the module conventions in the contribution docs
- [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
- [X]
@Emiller88 and @matthdsm thank you for the review. I'll work on it over the weekend.
@andersgs I think you didn't push your work? You added comments but there's no new commits. No rush, just wanted to review them if you were ready!
@Emiller88 that is true. I am working on adding the extra tests for different formats. I am also trying to work upstream to allow for compressed output. While the tool allows compressed input, it always outputs uncompressed output. I'll make the push as soon as I can get the test datasets into the test data repo.
@andersgs, are you still to work on this? No pressure, we're just cleaning up for the upcoming nf-core hackathon.