Merging GripHin Summary Reports with Varying Column Numbers

[mathavanpu]

Hi there,
I have 1,000 samples in our study and am running the Phoenix pipeline in batches of 100 samples each. The GRiPHin Summary for each batch contains a different number of columns based on AMR gene identification in the samples. How can I merge all the GRiPHin Summary reports into a single file? Is there a script or code available for this?

Thanks
Dr Mathavan Muthaiyan

[NoForkJustCommit]

Hi @mathavanpu thanks for you interest in PHX! We are working on a new release that will have a script to do this and tried to make sure it would be backwards compatible. We are working to get the release out as soon as possible, but it might be a few more weeks. In the meantime if you are feeling brave you can try the script out now, but be warned the branch is still under development so I wouldn't be surprised if you get an error and double check the results look correct. For your case here is the commands:

First, you'll need to pull the branch and then checkout a specific commit.

git clone -b v2.2.0-dev  https://github.com/CDCgov/phoenix.git
cd phoenix
git checkout 542c17ec8264d098b30a053b786226f2c150cf5b

Now you can reference the script (make sure you have the right path to wherever you saved the phoenix repo). Here --griphin_list needs a file that just the full path to each *_GRiPHin_Summary.xlsx file, one on each line.

phoenix/bin/combine_GRiPHins.py --output <new_file_prefix> --griphin_list <csv file> --bldb phoenix/assets/databases/BLDB_20250327.csv

Let us know if this works for you or if you run into an error.

[mathavanpu]

Hi, thank you for the response. I tried but encountered some errors. Please add some test data for test run

Command executed

phoenix/bin/combine_GRiPHins.py --output test --griphin_list *xlsx -b phoenix/assets/databases/BLDB_20250327.csv

usage: combine_GRiPHins.py [-h] [-g1 GRIPHIN_OLD] [-g2 GRIPHIN_NEW] [-o OUTPUT] -b BLDB
[-s SAMPLESHEET] [--griphin_list GRIPHIN_LIST]
[--coverage SET_COVERAGE] [--version]
Error message
combine_GRiPHins.py: error: unrecognized arguments: run3_batch_2_output_GRiPHin_Summary.xlsx run3_batch_3_output_GRiPHin_Summary.xlsx

[jvhagey]

We added a mode to do this. Can you try this nextflow run cdcgov/phoenix -r v2.3.0-dev -profile <your container of choice> --mode combine_griphins --input griphin_samplesheet.csv --outdir combined_griphins The input csv should just be a csv file with one line per full path to griphin files you want to combine.