Re-run Nextflow Muday time course data with SL4 and data downloaded from SRA

SRP460750

Directory: /projects/tomato_genome/fnb/dataprocessing/SRP460750/

Only SL5 was rerun with the SRA data and SL4 needs to be run with data as well.

For this task, we need to confirm and sanity-check the muday time course data that Rob recently uploaded and submitted to the Sequence Read Archive.
If the data are good, we will replace all the existing BAM, junctions, etc. files deployed in the "hotpollen" quickload site with newly processed data.
For this task:

• Check SRP on NCBI and review submission
• Download the data onto the cluster by using the SRP name
• Run nf-core/rnaseq pipeline
• Run our coverage graph and junctions scripts on the data

Note that all files should now use their "SRR" names instead of the existing file names.