Python script to import influenza results into labware 8

[tives82]

adding Python script to General_LW_scripts repo to import influenza sequencing results into labware 8

[tives82]

I've updated the script and it should be good for review now. Below you will find a summary of the changes that I made from the previous script.
To test it out, make sure you run the script within the flu directory and that the SampleSheet.csv file has been copied over from the run.

Required Files:
- SampleSheet.csv
- summary_report.tsv (walkercreek workflow output found in the 'SUMMARY_REPORT' directory)

Usage:
python influenza_labware8.py -r <summary_report.tsv> -s <SampleSheet.csv>

Changes:

• Improved filtering logic to exclude FLUSeq samples not found in summary_report.tsv from all output files (individual .txt, merged .txt, and summary .csv). This will also help find samples that failed sequencing or failed to produce viable fastq files.

• Now writes*missing LIMS_TEST_IDs to a separate *_missing_ids.txt file.

• Handles missing or partial clade column to avoid KeyError, assigning "No Nextclade Clade Detected" when necessary

• Ensures WGS Organism is set to "Influenza" for all included samples

• More robust handling of null values in IRMA fields (type, subtype, QC)

• Minor formatting/consistency fixes in logging and output

[erinyoung]

Can you add instructions and usage to the main readme as well?

[tives82]

I've updated the readme with made a small correction to the script name within the usage section.

[jwarnn]

Except for the lack of individual files, this script and the README make sense to me. Once you update the script so the individual files are created then I will approve PR.

[jwarnn]

Looks good now that I realize the individual txt files are in sub directory of the output folder.