Workflow for running fragpipe on impact trial test data

[rjcorb]

Purpose/implementation Section

What scientific question is your analysis addressing?

This PR adds required scripts, reference files, manifest, and workflow files to run fragpipe on IMPACT trial test data.

NOTE that there are still a few steps that need to be taken before this can be run:

• Download mzML files. These need to be downloaded from s3://bti-private-us-east-1-prd-impact-trial/source/. I think something like the following command should work from root:

  aws s3 cp s3://bti-private-us-east-1-prd-impact-trial/source/ impact-trial/ms-data/ \
    --recursive \
    --exclude "*" \
    --include "*.mzML"
  --exclude "PXD029082_2025-06-20/*"
  

After download, you should see 8 run-specific folders in the destination directory, each containing 8 mzML files corresponding to the 8 fractions.

• Obtain query fasta file. This can be obtained from the impact-trial repo: https://github.com/childrens-bti/impact-trial/blob/main/analyses/translation/results/custom_filtered.fasta. This file needs to be copied to impact-trial/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?

After downloading data into correct directory paths and pulling latest docker image, run fragpipe on impact trial data by executing the following from root:

cd impact-trial/
bash run_fragpipe_impact.sh --query [input_fasta]

Is there anything that you want to discuss further?

I am not sure how large of an ec2 instance this needs, but for reference I have run an a m6i.4xlarge. Our larger runs (with >100 CPTAC or HOPE samples) have required an instance of this size, but for a smaller data set it may not be required.

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 closing this PR since we are updating how fragpipe is run (see #25 ). I will update the wiki with instructions for downloading impact trial data.