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Clinical-Genomics-Lund / Pipeline-validation-tools

Set of tools for assisting verifications and validations.
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GIAB runner #1

Closed Jakob37 closed 1 week ago

Jakob37 commented 3 weeks ago

This is the first step of two, for setting up a system for easily running and evaluating changes in pipelines.

What it does:

python3 giab_runner.py \
  --outbase outbase \
  --repo /fs1/jakob/deploy/cmd_wgs \
  --checkout v3.10.3 \
  --label testrun \
  --config default.config \
  --run_type giab-single \
  --start_data bam

This will be followed by a second script which should be able to compare two output folders.

Ideally, this should be convenient enough such that it could be run for all minor/major deployments of the ol' wgs repo.

I have tested it to start both GIAB single and trio runs, and GIAB single from FASTQ, BAM and VCF.

Jakob37 commented 2 weeks ago

I have addressed and in most cases updated your comments @alkc . Do you want to take another look before merge?