Hello everyone. I'm running into an issue with the pipeline where the rmats workflow is getting skipped and I can't figure out why. I read the docs and I believe I have the appropriate parameters set so that the workflow will run. Below is my params file that I specify when launching the pipeline. Anyone have any suggestions why rmats wouldn't run? I see nothing in the .nextflow.log file about rmats.

{

"input": "mouse_sample_sheet1.csv",

"outdir": "<s3://XXXX/rnaseq/mouse_rnasplice/cortex/20240305_1>",

"gtf": "<s3://XXXX/ref/tg_mouse_hybrid_gtf_v2_2024-01-16.gtf>",

"fasta": "<s3://XXXX/ref/tg_mouse_hybrid_reference_v2.fa>",

"save_reference": true,

"contrasts": "contrasts1.csv",

"sashimi_plot": false,

"rmats": true,

"aligner": "star_salmon",

"dexseq_dtu": true,

"suppa": true,

"rmats_read_len": 151,

"rmats_paired_stats": false

}