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🧬 WGS-PRS Pipeline · clawbio | DecimalAI

scienceby clawbio

🧬 WGS-PRS Pipeline

clawbio/wgs-prs

Source clawbio/clawbio ↗License NOASSERTION

End-to-end WGS to polygenic risk score pipeline. Takes paired-end FASTQ files (or a pre-existing VCF) through nf-core/sarek for variant calling, applies VCF QC (normalisation, hard filtering, Ti/Tv and Het/Hom checks), then computes polygenic risk scores via the PGS Catalog. Fills the FASTQ to VCF gap upstream of the gwas-prs skill.

SkillScore88Maintained

Automatic

Clinical / Healthcare pack

Last verified 9/17/2026

What it changes

Passed 19 of 22 test cases with the skill, and 6 of 22 without it.

Without skill28%

With skill88%

Checks it passed that the model alone missed

Names claw-ancestry-pca
Directs the user to gwas-prs
Specifies the --no-fail-fast flag

and 21 more in the full report

15 fixed7 passed either way3 still failing0 broke

Pass-rate lift: +60 pp
Tokens: +58%
Agent turns: 0%
Response time: -46%

Model gemini-3.6-flashMeasured 9/17/2026v222 of 25 cases passed with skill · 22 comparable

Tokens, turns and time describe resource use, not a dollar price.

Use this skill

Save it into your project's skills folder. Claude Code picks it up in its next session.

curl -fsSL --create-dirs -o .claude/skills/clawbio-wgs-prs/SKILL.md https://app.decimal.ai/s/clawbio-wgs-prs/SKILL.md

Want it pinned and updatable? pip install "decimalai>=0.15", then decimalai skills add clawbio-wgs-prs, and start Claude Code with claude --plugin-dir "$(git rev-parse --show-toplevel)/.agents"

1 · One-time — install the CLI (docs ↗)

pip install "decimalai>=0.15"

2 · Get the skill — writes .agents/skills/clawbio-wgs-prs/ and pins it in .decimal/skills.lock

decimalai skills add clawbio-wgs-prs

No CLI? Get the same file — curl · raw file

curl -fsSL --create-dirs -o .claude/skills/clawbio-wgs-prs/SKILL.md https://app.decimal.ai/s/clawbio-wgs-prs/SKILL.md

Raw file: /s/clawbio-wgs-prs/SKILL.md ↗ · machine-readable summary at /s/clawbio-wgs-prs.json ↗

Safety checks: 3 of 3 passed

Code scan CleanIntent PassedContent Clean

See it in action

One of 15 test cases the skill fixed. Same model, same prompt, with and without the skill.

1 of 15

Prompt

What are the exact file names of the aggregated Markdown report and JSON summary generated in Stage 4?

What was checked, without and with the skill
Checked	Without skill	With skill
Names bridge_report.md as the Markdown summary file	Missed	Passed
Names bridge_report.json as the JSON summary file	Missed	Passed

case-23 · gemini-3.6-flash · 9/17/2026 · answers are capped and redacted

What's inside

The instructions your model reads when the skill loads.

SKILL.md205 linessingle file

🧬 WGS-PRS Pipeline

Author: David de Lorenzo (ClawBio Community) Requires: Python 3.9+, nextflow, docker or singularity, bcftools (recommended)

You are the WGS-PRS skill, an end-to-end pipeline agent for whole-genome sequencing data. Your role is to take a user from raw FASTQ files (or a pre-existing VCF) all the way to polygenic risk scores, with robust QC at every stage.

Trigger

Fire this skill when the user says any of:

"run WGS analysis"
"whole genome sequencing"
"FASTQ to PRS" / "FASTQ to polygenic risk scores"
"variant calling from raw reads"
"nf-core sarek" / "run sarek"
"germline variant calling"
"GATK HaplotypeCaller"
"raw sequencing to risk scores"
"WGS pipeline" / "WGS polygenic risk"

Do NOT fire when:

The user already has a VCF and wants PRS only: route to gwas-prs instead.
The user wants somatic variant calling (tumour/normal): out of scope, this skill handles germline only.
The user asks about microarray or SNP chip data: route to gwas-prs directly.
The user wants metagenomics or RNA-seq: wrong pipeline.

Scope

One skill, one task. This skill bridges raw WGS reads to polygenic risk scores via nf-core/sarek, VCF QC, and the ClawBio gwas-prs skill. It does not interpret clinical significance, annotate variants, or produce pharmacogenomics reports. Route those requests to variant-annotation, clinical-variant-reporter, or pharmgx-reporter.

Pipeline Stages

Variant calling: nf-core/sarek (FASTQ to BAM to VCF via GATK HaplotypeCaller)
VCF QC: bcftools normalisation, hard filtering, Ti/Tv and Het/Hom evaluation
PRS scoring: ClawBio gwas-prs skill (PGS Catalog, 6 curated + 3,000+ live scores)
Aggregated report: Markdown + JSON summary of all stages

Entry Points

Track record

Benchmark

19 / 22

test cases passed, vs 6 / 22 without

Adoption

Users: 3
Times used: 51

Safety and source details

SkillSafety

✓ 3 of 3 passed

Code scan15 of 15 checks clean

0 critical · 0 warning · 0 info — scanner v5 — 9/17/2026

View 15 scanner checks

live_secretremote_code_executionreverse_shelldata_exfiltrationssrf_metadataagent_snoopinganti_refusaldestructive_commandsobfuscated_unicodeunicode_homoglyphopaque_blobsuspicious_urltool_overreachtrigger_abuseprompt_injection_phrasing

IntentSafe

LLM judge · does the skill do what it claims

ContentClean

LLM judge · policy & harmful-content review

Source

Imported

clawbio / clawbio

skills/wgs-prs/SKILL.md

View on GitHub ↗

License MITImported 9/17/2026Version v2

More skills from the same source and nearby in the registry, with their headline benchmark lift.

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See it in action

What's inside

🧬 WGS-PRS Pipeline

Trigger

Scope

Pipeline Stages

Entry Points

Track record

Benchmark

Adoption

SkillSafety

Source

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