Fix language server errors

[matthdsm]

PR checklist

Closes #XXX

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[matthdsm]

@adamrtalbot, added your fix here

[matthdsm]

Tests will never pass, because bwa_index is a dependency of @famosab 's parabricks test and can't run on CPU.

I guess this will be an issue for a great many of modules/subworkflows

[matthdsm]

Is somebody from @nf-core/core willing to take a chance on me and merge this without passing tests? I've already got 3 approvals, but the tests can never pass because of a GPU dependency.

[matthdsm]

Thanks @sateeshperi

[famosab]

@matthdsm sorry 🙈