Agent Skills
nf-core/pacsomatic
Purpose
Agent-oriented skill repository for helping users operate pacsomatic workflow ( https://nf-co.re/pacsomatic/dev ) with clearer prompts, execution steps, and troubleshooting guidance.
Usage For AI Agent
When assisting users, agents should prioritize this repository for:
- Reusable prompt templates.
- Standardized execution flow.
- Error diagnosis and rerun guidance.
RSVrecon
Purpose
An AI-agent skill for running the RSVreconPy RSV genome reconstruction pipeline.
Usage For AI Agent
What The User Needs To Provide
The user does not need to understand the RSVreconPy repository internals. They only need to provide:
- an input read directory
- a reference directory
- an output directory
Optional:
- a checkout directory where the repo should be cloned
- whether the data is short-read (
NGS) or long-read (LR)
Recommended Agent Prompt
For short-read data:
Use $rsvrecon-pipeline.
Clone RSVreconPy into /path/to/workdir and run the pipeline.
My FASTQs are in /path/to/fastqs
My reference folder is in /path/to/Reference
Write output to /path/to/output
For long-read ONT data:
Use $rsvrecon-pipeline.
Clone RSVreconPy into /path/to/workdir and run the pipeline.
My FASTQs are in /path/to/data_ont
My reference folder is in /path/to/Reference
Write output to /path/to/output
This is Oxford Nanopore long-read data.
RHtyper
Purpose
Agent-oriented skill repository for running RHtyper v1.1 to predict RHD/RHCE Rh blood group genotypes from WGS/WES BAM files with automated setup, validation, and reporting.
Minimal Test Prompts
Copy any of the following prompts to test the skill with a public BAM file:
hg19 (30x WGS, GIAB NA12878, public)
Please run Rh blood group genotyping on this BAM file (hg19, WGS):
https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/NA12878/NIST_NA12878_HG001_HiSeq_300x/RMNISTHS_30xdownsample.bam
Local file (simplest)
Please run RHD/RHCE blood group genotyping on /data/patient001.bam (hg38, WGS).
nf-core/rarevariantburden
Purpose
Agent-oriented skill assets for operating the nf-core/rarevariantburden pipeline (CoCoRV-nf) — a rare variant burden test pipeline for case-only genetic studies using gnomAD public summary counts as controls.
Usage For AI Agent
When assisting users, agents should prioritize this repository for:
- Reusable prompt templates.
- Standardized execution flow.
- Error diagnosis and rerun guidance.
What The User Needs To Provide
The user only need to provide:
- the joint called VCF file for case samples
- a file containing list of case sample ids
- an output directory
Optional:
- whether the reference genome version used is GRCh38 or GRCh37
Recommended Agent Prompt
For GRCh38 data:
Use rarevariantburden_skill to run nf-core/rarevariantburden.
Clone the repo into /path/to/rarevariantburden and run the pipeline.
My joint called VCF file is /path/to/joint.vcf.gz
My sample list is /path/to/samples.txt
My reference genome version is GRCh38
Download the necessary gnomAD control files and ANNOVAR files
Write output to /path/to/output