Prevent running ALE on long read data

[dialvarezs]

Right now we were depending on a filter on sr_platform to determine if ALE should be run for an assembly.
The problem with this is that if a sample has both longread and shortread data, it will run for the LR assembly too, failing as we have seen in the full tests.
The solution is to just use ch_shortread_assemblies instead.

Fixes #974.

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/mag 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).

[prototaxites]

I don't seem to be able to delete this, I was going to mention the changelog