Fix ch_transcripts and ch_pubids for AWS

[avani-bhojwani]

The pipeline was running locally and on HPC, but failing tests on AWS even when run without fusion.

• Checking the errors indicated that it was probably be due to how ch_transcripts and ch_pubids were defined. They were using glob patterns. The pipeline now uses a different approach to create these channels. This has been tested by launching the AWS test action manually (for test profile).
• Upon fixing the issue above, the Transrate module was still not running on AWS, as it required a temporary directory. Creation of this directory is now included in the module.
• When running the full_test on AWS, it needs to be run without fusion or with less logs. If we don't do this, the fusion log files become too large during the Trinity module and the step is reattempted again and again with higher resources. I've added resource limits for full_test, so that we don't end up requesting >1TB of memory with reattempts.

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.