Remove requirement to provide reference fasta for Gen3-DRS download option

[Vlad-Dembrovskyi]

Description:

At the moment, if you want to download any bam or cram files from Gen3-DRS, you must rovide a fasta file. Fasta file is indeed need if you download cram files, but nowadays it is often (almost always) that you only download bam files, for which fasta is not needed.

Requirement for fasta is coded here: https://github.com/TheJacksonLaboratory/splicing-pipelines-nf/blob/ef65fe2ac92e22e657f1e7a7d31d35d2876f7e0e/main.nf#L358-L360

Task:

• comment this thing out with a note for future that it was commented out because we don't need it now but it may become relevant again in future
• represent the changes accordingly in documentation

[Vlad-Dembrovskyi]

What happens if we disable required fasta file, then indeed try to download a cram file? The pipeline will fail? If so, where? And how would we like to handle it? Have a check of the input file if it has crams or smth?

[Vlad-Dembrovskyi]

From Brittany:

Currently, I cannot find any RNA-seq cram options in GTEX, so it should never come up. I would think that it would fail at the bam to fastq step. However, we could always just check the extension on the file. (Is it a .bam?) I think we want the pipeline to fail for now.