bio-workflow-management-wdl-workflows
Create portable bioinformatics pipelines with Workflow Description Language (WDL) using Cromwell or miniwdl execution engines. Use when running GATK best practices pipelines, working with Terra/AnVIL platforms, or building workflows for cloud execution on Google Cloud or AWS.
npx skills add BioTender-max/awesome-bio-agent-skills --skill wdl-workflows --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: BWA 0.7.17+, FastQC 0.12+, GATK 4.5+, Nextflow 23.10+, Salmon 1.10+, Snakemake 8.0+, fastp 0.23+, samtools 1.19+ Before using code patterns, verify installed versions match. If versions differ: - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # WDL Workflows **"Build a WDL pipeline for Terra/AnVIL execution"** → Define tasks and workflows in WDL (Workflow Description Language) for execution on Cromwell, miniwdl, or cloud platforms (Terra, AnVIL) with built-in GATK best practices support. - CLI: `cromwell run workflow.wdl` or `miniwdl run workflow.wdl` for execution - WDL: version 1.0 task/workflow syntax with scatter-gather parallelism ## Basic Task Definition ```wdl version 1.0 task fastqc { input { File fastq Int threads = 2 } command <<< fastqc -t ~{threads} ~{fastq} >>> output { File html = glob("*_fastqc.html")[0] File zip = glob("*_fastqc.zip")[0] } runtime { docker: "biocontainers/fastqc:v0.11.9" cpu: threads memory: "4 GB" } } ``` ## Simple Workfl
- Version Compatibility
- Basic Task Definition
- Simple Workflow
- Task with All Sections
- Scatter (Parallel Execution)
- Scatter with Paired Files
- Conditional Execution
- Structs and Complex Types
- Input JSON
- Array Inputs JSON
- Subworkflows
- Runtime Options
- String Interpolation and Expressions
- File Size and Disk Calculation
Validate WDL syntax womtool validate workflow.wdl Generate inputs template womtool inputs workflow.wdl > inputs.json Run with Cromwell (local) java -jar cromwell.jar run workflow.wdl -i inputs.json Run with miniwdl (simpler local runner) miniwdl run workflow.wdl -i inputs.json Run on Terra Upload WDL and inputs.json to Terra workspace
What does the bio-workflow-management-wdl-workflows skill do?
Create portable bioinformatics pipelines with Workflow Description Language (WDL) using Cromwell or miniwdl execution engines. Use when running GATK best practices pipelines, working with Terra/AnVIL platforms, or building workflows for cloud execution on Google Cloud or AWS.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill wdl-workflows --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.