When transcript filtering is applied to GTF, the selected transcripts should also be used for transcriptome analyses

Is your feature request related to a problem? Please describe

• Consolidate transcript filtering with the transcriptome annotation: same set of transcripts used for GTF filtering to be used for transcriptome analyses

Describe the solution you'd like

1. When transcript filtering is applied to GTF, the selected transcripts should also be used for trancriptome mapping instead of 'longest transcript'

2. Need to modify 'find longest transcript' in general to select transcripts for all genes, not just protein coding.

3. The gtf file poduced by find longest transcript starts with 2 instead of 1.

Describe alternatives you've considered

• potentially the filtering module could be combined with the longest transcript module assignment

Additional context

Start by tracing the transcript filtering, transcriptome mapping, and “find longest transcript” workflow steps mentioned in the issue. Check how the selected transcripts flow into each analysis and inspect the generated GTF. Done means the filtered set is reused for transcriptome mapping, transcripts are selected for all genes, and the generated GTF starts correctly.