Issues

• Refactor remaining Snakemake run directives into debuggable scripts

  Daylily-Informatics/daylily-omics-analysis#151 · Filter by author iamh2o opened on Jun 3, 2026

• Evaluate upgrade to latest AWS ParallelCluster / pcluster 3.15.1

  Daylily-Informatics/daylily-omics-analysis#150 · Filter by author iamh2o opened on Jun 3, 2026

• Add explicit merge-by-barcode unit grouping for multi-lane FASTQ alignment

  Daylily-Informatics/daylily-omics-analysis#145 · Filter by author iamh2o opened on May 18, 2026

• Explore VEP stats flags for native MultiQC reporting with chunked VEP

  Daylily-Informatics/daylily-omics-analysis#144 · Filter by author iamh2o opened on May 18, 2026

• QC gap: Unified contamination thresholds across VerifyBamID2, GATK, and site_mix

  enhancementneeds-triageqc
  Daylily-Informatics/daylily-omics-analysis#139 · Filter by author iamh2o opened on May 4, 2026

• QC gap: Replace chr20 VerifyBamID2 resource with full-genome SVD marker panel for routine runs

  enhancementneeds-triageqc
  Daylily-Informatics/daylily-omics-analysis#138 · Filter by author iamh2o opened on May 4, 2026

• QC gap: Define microbial and viral read contamination screen governance

  enhancementneeds-triageqc
  Daylily-Informatics/daylily-omics-analysis#140 · Filter by author iamh2o opened on May 4, 2026

• QC gap: Add long-read platform QC for ONT and PacBio

  enhancementneeds-triageqc
  Daylily-Informatics/daylily-omics-analysis#137 · Filter by author iamh2o opened on May 4, 2026

• QC gap: Add cross-tool sample identity adjudication summary

  enhancementneeds-triageqc
  Daylily-Informatics/daylily-omics-analysis#134 · Filter by author iamh2o opened on May 4, 2026

• QC gap: Add HTD and pharmacogene QC summaries to MultiQC

  enhancementneeds-triageqc
  Daylily-Informatics/daylily-omics-analysis#135 · Filter by author iamh2o opened on May 4, 2026

• QC gap: Merge demux and lane QC context into downstream batch reports

  enhancementneeds-triageqc
  Daylily-Informatics/daylily-omics-analysis#136 · Filter by author iamh2o opened on May 4, 2026

• add deepsomatic rule

  Daylily-Informatics/daylily-omics-analysis#4 · Filter by author iamh2o opened on Aug 18, 2025

• Create VarNet Rule

  Daylily-Informatics/daylily-omics-analysis#3 · Filter by author iamh2o opened on Aug 18, 2025