Index files

[BarryDigby]

The workflow requires Hisat2 and STAR indices, and also a Kallisto and Salmon index file for downstream quantification. Using the test dataset chrI.fa file, figure out how to generate the index files and export them correctly from the process.

Like the kallisto example I showed you, which had the file parameter kallisto_index, only run these processes if the input index file is missing, and the reference genome/transcriptome file has been supplied.

To do

• kallisto index (transcriptome)
• salmon index (transcriptome)
• STAR index (genome)
• Hisat2 index (genome)
• Include the process TX for creating a transcriptome file - this is needed for kallisto and salmon.
• Include the appropriate ternary operators as conditionals so users can supply an index file to skip these steps upon re-running the workflow (e.g star_index, salmon_index which are file parameters in your config).
• Test locally before adding to main.nf and open a PR against BarryDigby/rtp_workshop (dev branch) when your continuous integration tests pass.