Outline

The intent with PipeEval is to make more in-depths evaluation of results between pipeline changes easier and faster to carry out.

Requirements

Written to be compatible with version 3.6 (the version running on our cluster).

Only standard libs are currently used.

Running the Runner

python3 main.py run \
    --checkout jw_update_genmod \
    --base out/genmod \
    --config default.config \
    --run_type giab_single \
    --start_data bam \
    --repo /path/to/repo \
    --label run1

Get more options by running:

python3 main.py run --help

Running the evaluator

python3 main.py eval \
    --results1 /path/results1 \
    --results2 /path/results2 \
    --config runner/default.config \
    --outdir /path/eval_out \
    --comparisons default

python3 main.py eval --help