TO-DO before upcoming release

[katsikora]

• [ ] createIndices: drop 'gtf to files', use gtfToGenePred instead? (would be consistent with repoTrampoline)
• [ ] take transcript2gene.txt as input to Salmon_Alevin ("genes_t2g")
• [ ] drop gene symbol annotation from velo_to_sce ? (scRNAseq_splitAlevinVelocityMatrices.R) - would relieve the requirement from gene ID to gene symbol mapping
• [ ] keep filterGTF and all downstream functions only for counting, not for mapping steps (or disable completely?)
• [ ] create salmon indices and update organism yamls