New module for KnotAnnotSV

[tetedange13]

Informations

New module for KnotAnnotSV : https://github.com/mobidic/knotAnnotSV

Tool do not have a Bioconda recipe nor a container, but is a collection of Perl script so added a simple git clone

Output files are not stable, so cannot use md5 in nf-tests

Added test-data, but waiting for nf-core/test-datasets#1905 to add correct links

PR checklist

• This comment contains a description of changes (with reason).
• 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.
• Broadcast software version numbers to topic: versions - See version_topics
• 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 (DO NOT HAVE DOCKER AVAILABLE)
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile micromamba

[itrujnara]

Hi, thanks for contributing to nf-core! Unfortunately, we cannot accept a git pull inside a module script, since this would make it impossible to run pipelines offline and could harm reproducibility. You can, however, add the tool to Bioconda yourself; one of the members has created a handy guide. In case you experience any issues, feel free to reach out on Slack.

[tetedange13]

Hi, thanks for contributing to nf-core! Unfortunately, we cannot accept a git pull inside a module script, since this would make it impossible to run pipelines offline and could harm reproducibility. You can, however, add the tool to Bioconda yourself; one of the members has created a handy guide. In case you experience any issues, feel free to reach out on Slack.

Thanks both of you for taking the time to explain me and review anyway !

I marked this PR as "draft" and will be back when I will have added tool to bioconda !

Best,
Felix.