WILDS Docker Library v0.1.0
We're excited to announce the first official release of the WILDS Docker Library — a centralized collection of Docker images for reproducible bioinformatics workflows, maintained by the Fred Hutch Data Science Lab (DaSL).
Highlights
- 48 Docker images covering alignment, variant calling, structural variants, annotation, RNA-seq, single-cell, QC, and more
- Multi-platform builds for linux/amd64 and linux/arm64 on most images (31 dual-platform, 17 AMD64-only)
- Dual registry publishing — all images available on both DockerHub and GitHub Container Registry
- Automated security scanning — vulnerability reports generated at build time and on a monthly schedule via Docker Scout
- Developer tooling — Makefile for local linting/building/validation, template Dockerfile, and comprehensive contributing guidelines
Docker Images
| Category | Images |
|---|---|
| Alignment | bwa, hisat2, star |
| Variant Calling | bcftools, gatk, strelka, varscan |
| Structural Variants | annotsv, delly, manta, smoove |
| Annotation | annovar, bedops, bedparse, bedtools |
| Copy Number | cnvkit, hmmcopy, ichorcna |
| RNA-seq | deseq2, rmats-turbo, rnaseqc, rseqc, salmon |
| Single-Cell | cellranger, scanpy, scvi-tools |
| QC & Processing | biobambam2, fastqc, picard, samtools, umitools |
| Data Download | awscli, ena-tools, gdc-client, sra-tools |
| Imputation | glimpse2 |
| Genomics | diamond, megahit, sourmash, spades |
| Specialized | arcpy, combine-counts, consensus, gtf-smash, jcast, python-dl, rtorch, shapemapper |
CI/CD Workflows
- Docker Build & Publish — automatically builds, tags, and pushes images on merge to
main - Dockerfile Linting — validates all Dockerfiles against best practices on every pull request
- Docker Scout Scanning — monthly vulnerability scans across all images with auto-generated CVE reports
Documentation
Feedback
This release is marked as a prototype — usable with support, but the API may change. We welcome feedback via GitHub Issues or email at wilds@fredhutch.org.
Full Changelog: https://github.com/getwilds/wilds-docker-library/blob/main/CHANGELOG.md