Telescope

[hanalysis]

PR checklist

Closes #9942

• If you've added a new tool - have you followed the module conventions in the contribution docs
• 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
• [See below] 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
    • [See below] nf-core modules test <MODULE> --profile conda

Regarding Bioconda - telescope already exists as a bioconda recipe (https://bioconda.github.io/recipes/telescope/README.html) however, several people (myself included) have found that this version no longer runs without some adjustments (see: mlbendall/telescope#44). I've found that telescope works with one minimal update, originally made by the author but never updated in conda (mlbendall/telescope@5d0325c). So I've made a docker image which just makes this minor update so the software can run. This seemed to me to be the most sensible way to proceed, but please let me know if there's something else I should do.

Lastly - telescope only produces output if there's any alignments with transposable element annotations, which there weren't with the test data. This is why my test just checks the log to ensure the run finished. Similarly, this just seemed like a pragmatic approach but do let me know if I should try something else.

Thanks!

[mashehu]

@nf-core-bot fix linting

[mashehu]

could you instead of providing you own docker container build it as a seqera container: https://nf-co.re/docs/tutorials/nf-core_components/using_seqera_containers

[mashehu]

something is off with the version capture. double check your sed command please 🙂

[prototaxites]

Regarding Bioconda - telescope already exists as a bioconda recipe (https://bioconda.github.io/recipes/telescope/README.html) however, several people (myself included) have found that this version no longer runs without some adjustments (see: mlbendall/telescope#44). I've found that telescope works with one minimal update, originally made by the author but never updated in conda (mlbendall/telescope@5d0325c). So I've made a docker image which just makes this minor update so the software can run. This seemed to me to be the most sensible way to proceed, but please let me know if there's something else I should do.

If there's no chance the author can be convinced to tag a new release, it might be worth trying to update the bioconda recipe to use this commit - bioconda recipes can be set up to pull on a particular commit of a repo instead of a particular tagged release.