skills.rest
bfairkun
bfairkunCOMMUNITY
Explore all skills by this author →
GitHub

new-project

Scaffolds RNA-seq analysis projects using the cookiecutter-quarto-smk template with snakemake submodules.

1|Updated Oct 25, 2020
Search Tags:#bioinformatics#project scaffolding#quarto#RNA-seq#Snakemake#cookiecutter#git submodules
One-click install
npx skills add https://github.com/bfairkun/dotfiles --skill new-project-bfairkun
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: new-project
Source: https://github.com/bfairkun/dotfiles/tree/main/agents/.agents/skills/new-project
Command: npx skills add https://github.com/bfairkun/dotfiles --skill new-project-bfairkun

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires cookiecutter.

What problem does it solve? Setting up a new RNA-seq analysis project involves repetitive boilerplate: creating directory structures, initializing git, and wiring up snakemake workflow submodules. This Skill automates that scaffolding with the cookiecutter-quarto-smk template so every project starts with a consistent Quarto+Snakemake layout. ## Core Features & Use Cases - Template-driven scaffolding: Runs cookiecutter against the cookiecutter-quarto-smk repository with documented defaults for every prompt (author, license, slurm partition, snakemake version). - RNA-seq submodule wiring: Configures the rna_seq snakemake workflow as a git submodule, including its nested submodules (GenometracksByGenotype, leafcutter, leafcutter2, leafcutter2_chao). - Non-interactive scripting: Supports --no-input mode with key=value pairs for fully automated project creation, including correct dict-literal syntax for the submodules parameter. - Use Case: A bioinformatician starting a new splicing analysis runs one command to create 20260310_MyProject with the standard analysis/, code/, data/, and output/ layout and the rna_seq workflow pre-linked. ## Quick Start Ask the AI to create a new RNA-seq project named with the YYYYMMDD_ProjectName convention using the cookiecutter-quarto-smk template and the rna_seq submodule.

Frequently Asked Questions about new-project

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I create a new RNA-seq project with cookiecutter?▼

Activate the cookiecutter conda environment and run cookiecutter against the cookiecutter-quarto-smk repository. Answer the prompts using the documented defaults, and for the submodules prompt pass a dict literal pointing to the snakemake-workflow_rna-seq repository.

How to run cookiecutter non-interactively with submodules?▼

Use --no-input with key=value pairs, passing submodules as a real Python dict literal such as {'rna_seq': {'url': '[email protected]:bfairkun/snakemake-workflow_rna-seq.git', 'branch': 'main'}}. The value is parsed with Python eval(), so it must be valid dict syntax.

What project naming convention should I use for cookiecutter projects?▼

Use the YYYYMMDD_ProjectName format for the project_name prompt, for example 20260307_naRNAseq_SSE. The repo_name prompt auto-lowercases this value and can be accepted as the default.

Why does cookiecutter fail with 'str' object has no attribute 'keys'?▼

This error occurs when the submodules value is passed as a string-in-string like "'{}'" instead of a bare dict literal "{}". Since submodules is parsed via eval(), the outer quoting must produce a dict, not a string containing a dict.

What directory structure does the cookiecutter-quarto-smk template create?▼

It creates analysis/ for Quarto notebooks, code/module_workflows/rna_seq as a git submodule, code/rules for project-specific snakemake rules, plus data/ and output/ directories. The project is initialized as a git repository inside the projects directory.

Related Skills

Explore More Education & Research Skills→
dmccrearydmccreary
90

install-mkdocs-template

Create an MkDocs Material project scaffold with Conda and GitHub Pages.

Community
Advanced
estebandegetauestebandegetau
1

quarto-style

Enforce Quarto style and authoring conventions for .qmd files.

Community
Intermediate
JamesFincherJamesFincher

jupyter-live-kernel

Execute Python code against a persistent live Jupyter kernel.

Community
Intermediate
htlin222htlin222
77

quarto-book

Generate a Quarto Book project structure with customizable chapters, author, and title.

Community
Basic