Hi all, could you please share your thoughts on why the RNA splice pipeline failed on these two tasks with these error messages? I've attached screenshots of the sample sheet and contrast sheet.

NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:CLUSTERGROUPS_IOI

NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:CLUSTERGROUPS_IOE

Error message( from .command.err file):

Traceback (most recent call last):
  File "/mnt/batch/tasks/workitems/job-8f2fe2901cf7e8b46542-NFCORE_RNASPLICE_RNASPLICE_SUPPA_SALM/job-1/nf-ee207d539af4a602a153432074ab37bf/wd/.nextflow-bin/suppa_groups.py", line 48, in <module>
    main(args)
  File "/mnt/batch/tasks/workitems/job-8f2fe2901cf7e8b46542-NFCORE_RNASPLICE_RNASPLICE_SUPPA_SALM/job-1/nf-ee207d539af4a602a153432074ab37bf/wd/.nextflow-bin/suppa_groups.py", line 35, in main
    assert len(out) == 2, "Column numbers have to be continuous, with no overlapping or missing columns between them."
AssertionError: Column numbers have to be continuous, with no overlapping or missing columns between them.

Hey @BiologyGeek I'm not sure. I'm not sure I'm the best person to help with this, could you give me some more info on how I could help?

Thank you @Edmund for your response. My question is, does this sample sheet and contrast sheet meet the minimum requirements for a successful RNA splice pipeline run? Am I missing something in the design of the contrast sheet that led to this issue?

Disclaimer: I've never used rnasplice myself. I'd try taking the `.`'s out of the your treatments and make them `_`'s maybe?

I greatly appreciate your input; let me give it a try. Could you please guide me to someone experienced with RNA splice pipeline who might be able to answer potential future questions?

Looks like @Ben Southgate and @James Ashmore would be good people to ask. You might open a GitHub issue as well with your original message and anything else you've tried for tracking! https://github.com/nf-core/rnasplice/issues/new/choose

Hey @BiologyGeek Please could you open an issue on the GitHub repository if you are still encountering an issue? The profiles linked by @Edmund are unfortunately no longer active as they were created with our previous employer's work email addresses.