Fix plugins for features that do not support transcript

[bartcharbon]

vcf/aip | PASSED | 193482=completed output/vcf/aip/.nxf.log vcf/chd7 | PASSED | 193483=completed output/vcf/chd7/.nxf.log vcf/corner_cases | PASSED | 193484=completed output/vcf/corner_cases/.nxf.log vcf/deb_register | PASSED | 193485=completed output/vcf/deb_register/.nxf.log vcf/empty_input | PASSED | 193486=completed output/vcf/empty_input/.nxf.log vcf/empty_output_filter_samples | PASSED | 193487=completed output/vcf/empty_output_filter_samples/.nxf.log vcf/empty_output_filter | PASSED | 193488=completed output/vcf/empty_output_filter/.nxf.log vcf/filter_samples | PASSED | 193489=completed output/vcf/filter_samples/.nxf.log vcf/liftover | PASSED | 193490=completed output/vcf/liftover/.nxf.log vcf/multiproject_classify | PASSED | 193491=completed output/vcf/multiproject_classify/.nxf.log vcf/mvid | PASSED | 193492=completed output/vcf/mvid/.nxf.log vcf/trio | PASSED | 193493=completed output/vcf/trio/.nxf.log vcf/vkgl_lb | PASSED | 193494=completed output/vcf/vkgl_lb/.nxf.log vcf/vkgl_lp | PASSED | 193495=completed output/vcf/vkgl_lp/.nxf.log

End-to-end tests are not executed by Travis CI, please execute manually:

• [ ] APPTAINER_BIND=$PWD bash test/test.sh passes
• [ ] Updated documentation