Update the aligners (bowtie2, bwa, chromap and star) and associated steps processing steps to use topics channel for software versions.

[Kevin-Brockers]

• This is a bit of a bigger update. Mainly due to combining fasta channels with their index (ch_fasta_fai) in samtools modules.

1. Synced and version dumped the aligners (bowtie2, bwa, chromap and star)
   • Main purpose was to utilize topics channel for software versions
2. Adapted more of the pipeline to handle also updated samtools packages
   • Main change was to go from ch_fasta to ch_fasta_fai.
   • When ever possible the previous ch_fasta and ch_fai were combined, if not needed dummy channels were created.
3. Additionally, changed a channel operators (e.g branch - legacy) to a typed solution.