Adding initial version of ww-fastp WILDS WDL module

[tefirman]

Type of Change

• New module

Description

Adds ww-fastp, a new WILDS WDL module wrapping fastp, an ultra-fast all-in-one FASTQ preprocessor. fastp performs quality filtering, adapter trimming, and comprehensive QC reporting in a single pass, making it a fast alternative to tools like Trimmomatic or Cutadapt.

The module includes two tasks:

• fastp_paired — Paired-end FASTQ preprocessing with adapter auto-detection
• fastp_single — Single-end FASTQ preprocessing

Also removes two unused linting rules (CommentWhitespace, TrailingComma) from sprocket.toml that were generating warnings.

Testing

How did you test these changes?
Ran make lint NAME=ww-fastp (sprocket, miniwdl, WOMtool all pass) and make run_sprocket NAME=ww-fastp using ww-testdata paired-end FASTQ files. Trimmed FASTQs and HTML/JSON QC reports were generated successfully.

What workflow engine did you use?
Sprocket v0.22.0

Did the tests pass?
Yes — linting clean across all three linters and testrun completed successfully.

Documentation

• I updated the README (if applicable)
• I added/updated parameter descriptions in the WDL (if applicable)
• I ran make docs-preview to check documentation rendering (if applicable)

Additional Context

• Uses Docker image getwilds/fastp:1.1.0 from Docker Hub
• Test workflow uses relative imports for local development; these should be updated to GitHub raw URLs before merging

[emjbishop]

Just some minor comments