Fix mito QC stats JSON conversion crash for bam started-runs when BAM-derived sample id deviates from rerun sample id

[alkc]

Description and reviewer info

Update to process and python script that converts mito sentieon coverage TSV to JSON.

The script previously required sample-id input to properly access specific fields in the TSV.
This has now been changed so that the same values are accessed by suffix, under the strong
assumption that the TSV contains data from only one sample.

Fixes #169

Type of change

• Documentation
• Patch
• Minor change
• Major change

Checklist

• Self-review of my code
• Update the CHANGELOG
• Tag the latest commit (vX.Y.Z format)
• Log samples used for testing in the Verification_samples_log Excel sheet

Minor change / patch-ish

• bam-started wgs run completes with custom sample id and mito QC data checks out
• wgs trio run completes started from bjorn/fastq and mito QC data checks out for all samples
• Updated mito script fetches the correct values and outputs correct JSON to stdout
• At least one other person has reviewed and approved my code
• I have made corresponding changes to the documentation (software versions, etc.)

Test/review documentation

Review performed by

• Alexander
• Jakob
• Paul
• Ryan
• Viktor

(Add if missing)

Testing performed by

• Alexander
• Jakob
• Paul
• Ryan
• Viktor

[Jakob37]

Looks good!

Just some small reflections.

[Jakob37]

dict[str, str] ?

[alkc]

nope. the python3 in our wgs singularity container is too old for that.

typing.Dict might work though. i'll check.

[Jakob37]

You could try this:

https://peps.python.org/pep-0585/

I.e. importing

from __future__ import annotations

And then

dict[str, str]

Not sure it works. But curious to know

[alkc]

Script confirmed to work for commit 844ae20:

Singularity wgs_active.sif:/mnt/beegfs/nextflow/GIAB... > cat ./GIAB-NA24385-D1-230622-20240924_mito_coverage.tsv | cut -f 5,9                                           
GIAB-NA24385-D1-230622_mean_cvg GIAB-NA24385-D1-230622_%_above_500                                                                                                                                                                                 
24654.35        100.0                                                                                                                                                                                                                              
Singularity wgs_active.sif:/mnt/beegfs/nextflow/GIAB... > python3 /fs1/alkc/proj/nextflow_wgs/bin/mito_tsv_to_json.py ./GIAB-NA24385-D1-230622-20240924_mito_coverage.tsv
{                                                                                                                                                                                                                                                  
    "mito_qc": {                                                                                                                                                                                                                                   
        "mean_coverage": 24654.35,                                                                                                                                                                                                                 
        "pct_above_x": {                                                                                                                                                                                                                           
            "500": 100.0                                                                                                                                                                                                                           
        }                                                                                                                                                                                                                                          
    }                                                                                                                                                                                                                                              
}                                                                                           

[alkc]

Scrpt confirmed to work for commit 844ae20 in wgs trio.

[alkc]

I'm omitting scout testing here, as this part of the pipeline does not affect scout loads.

I've confirmed that the QC data for CDM is a merged parseable json for both wgs single and trio.

[alkc]

The update resolves one particular obstacle in bam-started pipeline runs, but there is work remaining that will have to be resolved in a separate patch: #233