wdlfmt 0.1.0

Formatter for WDL files

wdlfmt — a formatter for Workflow Description Language (WDL)

wdlfmt is an opinionated, lossless formatter for WDL v1.0 that enforces consistency and targets the BioWDL Style Guidelines.

For now there is no automated way of styling or checking the style of WDL files according to these guidelines. — BioWDL Style Guidelines

wdlfmt aims to solve this problem.

Installation

git clone https://github.com/Chris1221/wdlfmt.git
pip install -e wdlfmt

Or with pixi:

git clone https://github.com/Chris1221/wdlfmt.git
cd wdlfmt && pixi install

Usage

By default, formatted output is written to stdout and a style compliance checklist is printed to stderr:

wdlfmt my_task.wdl

Format in place with -i:

wdlfmt -i my_task.wdl

Suppress the checklist with --no-check:

wdlfmt --no-check my_task.wdl

Redirect formatted WDL to a file while keeping the checklist visible:

wdlfmt my_task.wdl > formatted.wdl

What the formatter does

wdlfmt rewrites WDL files with consistent style, preserving all comments:

Rule	Example (before → after)
4-space indentation	tabs / mixed spaces → 4 spaces
Heredoc command syntax	command { ... } → command <<< ... >>>
Double-quoted strings	'hello' → "hello"
Spaces around =	key=value → key = value

BioWDL style compliance checklist

After every format run, wdlfmt emits a per-rule checklist to stderr. Rules the formatter enforces are shown as confirmed guarantees; content rules that depend on the file's naming and structure are checked and reported:

BioWDL Style Guide Compliance
──────────────────────────────────────────────────────
  Formatter guarantees
    ✓  4-space indentation
    ✓  Heredoc (<<<) command syntax
    ✓  Double-quote string literals
    ✓  Spaces around = operator
  Content checks
    ✓  Task names are UpperCamelCase
    ✓  Workflow names are UpperCamelCase
    ✓  Struct names are UpperCamelCase
    ✗  Call aliases are lowerCamelCase
         Non-conforming aliases: myAlias
    ✓  Line length ≤ 100 chars
    !  set -e -o pipefail in multi-command blocks
         Missing in: block 1
    !  parameter_meta section present
         Missing in: task 'MyTask'
    ✓  docker defined in runtime blocks
──────────────────────────────────────────────────────
  1 failed  ·  2 warning(s)  ·  9 passed

Symbols: ✓ pass · ✗ fail (rule violated) · ! warn (advisory)

Content rules

Rule	Level	Description
Task names are UpperCamelCase	fail	task myTask → rename to MyTask
Workflow names are UpperCamelCase	fail	Same convention for workflows
Struct names are UpperCamelCase	fail	Same convention for structs
Call aliases are lowerCamelCase	fail/warn	call Foo as Bar fails; call Foo (no alias) warns
Line length ≤ 100 chars	fail	Reports offending line numbers
set -e -o pipefail in command blocks	warn	Advisory for multi-command blocks
parameter_meta section present	warn	Advisory per task/workflow
docker in runtime blocks	warn	Advisory per runtime block

Python API

import wdlfmt

# Format a WDL string
formatted = wdlfmt.format_wdl_str(wdl_text)

# Run the style checker on already-formatted text
results = wdlfmt.check_style(formatted)
for r in results:
    print(r.rule, r.status.value, r.details)