Re-run Nextflow Muday time course data again with SL5 and data downloaded from SRA

SRP460750

Directory: /projects/tomato_genome/fnb/dataprocessing/SRP460750/nfcore-SL5-2024-05-07

Previously we noticed that SRA had mismatched some of the data incorrectly and 16 of the sample-names were mislabeled. Dr. Reid reached out and had SRA change everything to the correct sample names. Now we must rerun the muday SRA data again on the cluster with nextflow and make sure the data is correctly labeled.

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.