CPG Flow Stripy

#--image australia-southeast1-docker.pkg.dev/cpg-common/images/cpg-flow-stripy:0.2.2-1 A CPG workflow for creating STR reports with STRipy, using the cpg-flow pipeline framework.

Purpose

This workflow is designed to process short-read sequencing data and create reports with STRipy.

The short-read data is processed at the sequencing group level, and STRipy reports are generated for each sequencing group. The configuration allows complete customisation as to which STR loci are analysed and which reports are created.

Example invocation

analysis-runner \
    --skip-repo-checkout \
    --image australia-southeast1-docker.pkg.dev/cpg-common/images/cpg-flow-stripy:0.2.2-1\
    --config src/cpg_flow_stripy/config_template.toml \
    --config stripy_loci.toml \  # containing the inputs_cohorts and sequencing_type
    --dataset seqr \
    --description 'stripy' \
    --access-level standard \
    --output-dir stripy_run_<date> \
  run_workflow

Requirements

• Clone the production-pipelines-configuration repository to a known location and ensure the stripy config files are used in the analysis-runner submission.

CPG Flow STRipy Pipeline

stages

1. RunStripy

   1. Call stripy to run STR analysis on all available loci. Produces a JSON & HTML with findings for all loci, but the HTML is not extracted.

2. MakeStripyReports:

   1. Leverage the Loci presets and the per-dataset subset selection config file (see prod-pipes-config).
   2. Ingest the all-Loci JSON file, and for each requested subset for a Dataset, create a separate HTML, containing only the appropriate Loci
   3. For each report record any instances of a Locus being selected, but not being available in the callset

3. MakeIndexPage

   1. DatasetStage, collects all reports generated for the SGs in a Dataset, and creates one Index page
   2. The index page contains the SG & Family ID, the report sub-type, the link to the report, and any missing loci relative to the documented Loci subset