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WILDS WDL Library v0.2.0

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@tefirman tefirman released this 30 Mar 19:39
· 75 commits to main since this release
v0.2.0
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WILDS WDL Library v0.2.0

We're excited to announce the second release of the WILDS WDL Library, featuring significant growth in both the library's content and its contributor community.

Highlights

  • 44 Modules (up from 33) covering alignment, variant calling, structural variants, annotation, RNA-seq, QC, assembly, protein structure, and more
  • 12 Pipelines (up from 8) ranging from basic to advanced production-ready workflows
  • 12 Contributors — the library has grown from a core team effort to a collaborative project with contributions from researchers across Fred Hutch, driven by the new WILDS WDL Development Program
  • Cirro Integration — multiple pipelines now include platform-specific configurations for cloud execution on Cirro

New Modules (since v0.1.0)

Category Modules
Alignment ww-bowtie, ww-bowtie2
Variant Calling ww-deepvariant
RNA-seq ww-fastp, ww-jcast, ww-rmats-turbo
Protein Structure ww-colabfold, ww-starling
Coverage & Visualization ww-deeptools
Geospatial ww-sjl
Imputation ww-glimpse2

New Pipelines (since v0.1.0)

Pipeline Description Complexity
ww-imputation Genotype imputation from low-coverage WGS using GLIMPSE2 Intermediate
ww-jetlag Solar Jetlag tile processing across geographic tiles Basic
ww-splicing-proteomics Alternative splicing proteomics with STAR, rMATS, and JCAST Intermediate
ww-starling-batch Batch protein ensemble generation using STARLING Basic

Cirro Configurations

The following pipelines now include .cirro/ platform configurations for cloud execution:

  • ww-bwa-gatk
  • ww-fastq-to-cram
  • ww-imputation
  • ww-saturation
  • ww-splicing-proteomics
  • ww-sra-salmon

WILDS WDL Development Program

This release marks the first to include contributions from the WILDS WDL Development Program, a collaborative initiative where Fred Hutch researchers partner with the OCDO Research Informatics team to convert their computational analyses into production-quality WDL workflows. Several of the new modules and pipelines in this release originated from researcher collaborations through the program.

Infrastructure Improvements

  • Added Dockstore integration via .dockstore.yml for workflow discoverability
  • Added CITATION.cff for proper citation support
  • Automated Cirro configuration validation in CI/CD
  • Updated execution engine versions in CI/CD

Documentation

Feedback

We welcome feedback via GitHub Issues or email at wilds@fredhutch.org.

Full Changelog: https://github.com/getwilds/wilds-wdl-library/blob/main/CHANGELOG.md

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