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
CAB-aiSkills
Portable agent skills from the CAB-aiSkills toolbox (St Jude CAB). Each skill is a self-contained folder with SKILL.md, scripts, and documentation for Cursor and other agent clients.
volcano-grid-plot
Purpose
Build publication-ready grids of Volcano and/or MA plots from multiple differential gene-expression or differential binding tables (RNA-seq, ChIP-seq, ATAC-seq, Cut&Run, multi-omics). Auto-detects or harmonizes column names for log2FC, p-value/FDR, gene/region IDs, and average expression; supports highlighting genes of interest.
Usage For AI Agent
When assisting users, agents should use this skill for volcano plot grids, MA plot grids, multi-panel DE figures, or timecourse differential visualization.
Example prompt:
Plot GSE202762 EGF timepoints from volcano-grid-plot/examples in natural order as a volcano grid. Highlight EGR1 on volcano and MA figures.
kde-correlation-scatter
Purpose
Generate a publication-quality 2D scatter plot with KDE density background comparing two differential experiments (RNA-seq, ChIP-seq, ATAC-seq, Cut&Run, or mixed multi-omics). Supports annotation-vs-annotation, region-vs-region, and rank-vs-rank modes with Pearson/Spearman correlation and quadrant counts.
Usage For AI Agent
When assisting users, agents should use this skill for 2D scatter plots, KDE correlation plots, directional p-value plots, rank-rank correlation, or comparing two differential result files.
Example prompt:
Make a KDE correlation scatter comparing contrast_A.regulation.tsv and contrast_B.regulation.tsv using directional p-values; write figures under ./plots.
reproducible-peaks
Purpose
Generate reproducible ChIP-seq or ATAC-seq peak sets across biological replicates with ChIP-R from narrowPeak, broadPeak, or SICER BED inputs. Infers MACS2 with/without control (noC_), broad peaks, and SICER conversion; logs commands and environment for reproducibility.
Usage For AI Agent
When assisting users, agents should use this skill for reproducible peaks, ChIP-R, ChIP-seq replicate overlap, narrowPeak/broadPeak merging, or CTCF/histone replicate peak sets.
Example prompt:
Generate reproducible CTCF peaks with ChIP-R using the two BED files in reproducible-peaks/examples and save outputs under agentResults/.
pathway-enrichment-enrichr
Purpose
Run Enrichr pathway enrichment for one gene list or many lists (GMT or TSV manifest). Produces merged tables, Excel workbooks, PDF bar charts for top pathways, and for batch runs heatmaps and dot plots.
Usage For AI Agent
When assisting users, agents should use this skill for Enrichr pathway enrichment, GO/KEGG/Reactome enrichment tables, GMT batch enrichment, multi-sample pathway dot plots or heatmaps, or exporting enrichment results to Excel/PDF.
Example prompt:
Run Enrichr pathway enrichment on my gene list genes.txt, use library preset stjudehg, and write Excel summaries and PDF bar plots under ./enrichr_out.
tables-to-excel
Purpose
Merge CSV, TSV, or tab-delimited TXT tables into a single multi-sheet .xlsx workbook with a first-sheet NameDictionary mapping each worksheet name to the absolute path of its source file for provenance and auditability.
Usage For AI Agent
When assisting users, agents should use this skill to consolidate DEG tables, gene lists, QC summaries, or any flat tables into one shareable Excel bundle without manual copy-paste.
Example prompt:
Merge table1.tsv, table2.csv, and table3.txt into one Excel file with a NameDictionary sheet; save as ./combined_tables.xlsx.