Docker-first / Reproducible

UhlemannLab Pipeline Hub

Practical runbook for containerized pipeline operation in real lab workflows.

Design Goal

All pipelines are containerized and designed for reproducible execution: fixed entry scripts, mounted host data paths, and predictable output folders.

Pipeline Summary

Available now

longWGS

ONT assembly, polishing, QC, coverage, and annotation.

 Available now

shortWGS

Illumina typing with MLST/ARG/Plasmid/TETyper and report outputs.
In testing

PFsnake

P. falciparum variant/CNV/drug summary pipeline.

In testing

RNake

Bacterial RNA-seq processing and count-table generation.

In testing

TnSeq_ONT

ONT flank extraction and clustering workflow.

Reproducibility Notes

  • Docker is the default runtime for all wrappers.
  • Input and database paths are mounted from host paths.
  • Each wrapper supports dry-run mode for plan validation.
  • Progress and lock-retry behavior are integrated in wrappers.