sahuno
@sahuno
Public Skills
snakemake
by sahuno
Expert Snakemake workflow engineer for bioinformatics pipelines on SLURM HPC. Specializes in creating, debugging, and running Snakemake 9 workflows with battle-tested SLURM profiles, proper container integration, and reproducible run organization. Use this skill proactively whenever the user asks to: create/write/build a Snakemake workflow or pipeline, debug a Snakemake error or failed SLURM job, add rules to an existing Snakefile, write or fix a SLURM profile for Snakemake, organize pipeline outputs or run directories, convert a shell script or ad-hoc analysis into a reproducible Snakemake workflow, or troubleshoot Snakemake 9 + SLURM executor issues (memory conflicts, container propagation, stale locks). Also trigger when the user mentions snakemake dry-run, snakemake DAG, snakemake profile, workflow-profile, SLURM executor plugin, modkit pileup pipeline, or any multi-sample bioinformatics pipeline that needs per-sample parallelism with a dependency DAG. Do NOT trigger for: tasks with <3 steps and no parallelism (bash script is better), pure Nextflow workflows, or one-off data exploration.
igv-screenshots
by sahuno
This skill generates IGV screenshots using igver for genomic visualization. Use when user asks to "take IGV screenshot", "IGV snapshot", "visualize BAM in IGV", "igver screenshot", "show me the reads at", "screenshot genomic region", "visualize methylation in IGV", "IGV plot of BAM", "generate IGV images", "look at this region in IGV", "screenshot structural variant", "haplotype visualization in IGV", or any mention of IGV/igver with BAM files. Handles Singularity/Docker execution, chromosome naming mismatches, methylation coloring (ONT/PacBio), and batch generation for large region sets.
heatmap-dimensions
by sahuno
This skill creates publication-quality heatmaps with automatically calculated dimensions for Nature journal specifications. Use when user asks to "create a heatmap", "make a DE gene heatmap", "plot expression heatmap", "heatmap with proper dimensions", "clustered heatmap", "gene expression heatmap", "correlation heatmap", "heatmap for DESeq2 results", "ComplexHeatmap", "pheatmap with correct size", or any mention of heatmap visualization. Automatically calculates optimal height based on number of genes (rows) and determines whether to show row labels. Fixed width of 180mm for publication quality. Supports DESeq2, correlation matrices, and clustering analysis.
barplot-long-labels
by sahuno
This skill creates publication-quality horizontal barplots with long categorical y-axis labels. Use when user asks to "create a GO enrichment barplot", "make a barplot with pathway names", "plot KEGG results as horizontal bars", "barplot with long y-axis labels", "enrichment figure with proper dimensions", "horizontal barplot that fits all labels", or needs help sizing figures with long text on the y-axis. Automatically calculates optimal width and height based on label length and number of categories. Supports GO, KEGG, Reactome pathway visualization.