Fragpipe CPTAC run for tumor-enriched splice event-derived peptides

[rjcorb]

Purpose/implementation Section

What scientific question is your analysis addressing?

I've created a tumor-specific-splicing repo for TMT quantification of AS event-derived peptides in CPTAC and HOPE proteomics data. Current functionality just supports quantification using CPTAC data as input.

What was your approach?

What GitHub issue does your pull request address?

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

Steps to run this code:

1. Pull docker image following instructions in README.
2. Follows Steps 1-2 in the repo wiki to run the docker container in --privileged mode and configure sbfs credentials for cavatica project mounting. NOTE: you do not need to mount project here, it is now done within the fragpipe bash script.
3. cd into /home/rstudio/fragpipe/tumor-enriched-splicing and run the following command:

bash run_fragpipe.sh --run_subset

Is there anything that you want to discuss further?

I am currently getting the following error when running the above code:

2025-09-05 19:21:45,475 ERROR - Duplicate samples found in annotation files. The sample names must be unique among all experiments. 

I believe this is related to us updating Fragpipe versions. We previously ran this same workflow using v22.0 and had no issues, but now we are getting this error with 23.1. You will see that there is only a single annotation file in the tmp/01CBTTC_PBT_Proteome_HMS_20180626/ directory and that all sample labels are unique. So I really don't know what could be going on here.

I submitted an issue to the fragpipe developers, but they were not able to diagnose the issue: Nesvilab/FragPipe#2423

Someone else also reported a getting the same error after updating to Fragpipe 23.1. It is unclear if they resolved the issue, and they also seem to have run this in the GUI rather than via command line: Nesvilab/FragPipe#2276

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

Results

What types of results are included (e.g., table, figure)?

What is your summary of the results?

Reproducibility Checklist

• The dependencies required to run the code in this pull request have been added to the project Dockerfile.

Documentation Checklist

• This analysis module has a README and it is up to date.
• The analytical code is documented and contains comments.

[rjcorb]

@jharenza I am closing this PR since #25 will update fragpipe such that all files (manifest, workflow, fasta) will be supplied via command line.