Fix transrate dependencies issue

[avani-bhojwani]

The pipeline uses Transrate from the Oyster River Protocol. Previously, I had created a Dockerfile to be able to use this. However, it does not have all the dependencies needed. Turns out there is already a Docker container available for the Oyster River Protocol. So, the pipeline will use that as suggested by (#31) .

I've also added the transrate_reference param to the test configs to make it easier to check the utility of this module (nf-core/test-datasets#1450).

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 pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/denovotranscript branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[nf-core-bot]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.1.0.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.