Copier

[schnea]

Summary by CodeRabbit

Release Notes

• New Features

  • Added project templating system enabling customizable project names and feature selection.
  • Introduced example workflow demonstrating simplified input/output handling.

• Updates

  • Simplified configuration structure with refined ignore patterns.
  • Enhanced Git handling through improved file tracking.

[coderabbitai]

Caution

Review failed

The pull request is closed.

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 75bd70d4-9c85-401b-bcbc-d281fe9e1b5d

📥 Commits

Reviewing files that changed from the base of the PR and between edc3127 and ae92164.

📒 Files selected for processing (24)

• .gitattributes
• .gitignore
• .test/config/config.yaml
• config/config.yaml
• copier.yml
• workflow/envs/simulate_reads.yaml
• workflow/envs/validate_genome.yaml
• workflow/rules/common.smk
• workflow/rules/process_reads.smk
• workflow/schemas/samples.schema.yaml
• workflow/scripts/validate_fasta.py
• {{ project_name }}/.gitignore
• {{ project_name }}/.snakemake-workflow-catalog.yml
• {{ project_name }}/LICENSE
• {{ project_name }}/README.md.jinja
• {{ project_name }}/config/README.md
• {{ project_name }}/config/config.yaml
• {{ project_name }}/data/config.yaml.jinja
• {{ project_name }}/data/input.txt
• {{ project_name }}/profiles/README.md
• {{ project_name }}/workflow/Snakefile
• {{ project_name }}/workflow/envs/get_genome.yaml
• {{ project_name }}/workflow/rules/example.smk
• {{ project_name }}/workflow/schemas/config.schema.yaml

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📝 Walkthrough

Walkthrough

This PR simplifies a Snakemake workflow template by removing complex read simulation, genome validation, and FastQC analysis rules, replacing them with a minimal example copy rule. It adds template configuration via copier.yml, updates Git attributes, and reorganizes ignore patterns to focus on pixi environments.

Changes

Cohort / File(s)	Summary
Git and Build Configuration .gitattributes, .gitignore	Updated .gitattributes for pixi.lock syntax highlighting with binary merge behavior; revised .gitignore to focus on pixi environments (.pixi/*) while tracking .pixi/config.toml, removing broad patterns for results, logs, and test outputs.
Test and Main Configuration .test/config/config.yaml, config/config.yaml	Simplified configuration by removing sample_sheet, genome retrieval (get_genome.ncbi_ftp), and read simulation parameters (simulate_reads.read_length, read_number); replaced with single input_file reference in test config.
Workflow Rule Removal workflow/rules/process_reads.smk, workflow/rules/common.smk	Eliminated complex workflow rules (get_genome, validate_genome, simulate_reads, fastqc, multiqc) and sample DataFrame loading/validation logic; removed schema-based validation imports.
Environment and Schema Files workflow/envs/simulate_reads.yaml, workflow/envs/validate_genome.yaml, workflow/schemas/samples.schema.yaml, workflow/scripts/validate_fasta.py	Removed conda environment specifications, YAML schema definition for samples, and FASTA validation script.
Template System Configuration copier.yml	Added new template configuration with project_name and features input fields (isolated conda environments, Jupyter Notebook Integration, Report Generation, Schema Validation) with placeholder sections for future extensions.
Template Content Files {{ project_name }}/workflow/Snakefile, {{ project_name }}/workflow/rules/example.smk	Replaced workflow includes (common.smk, process_reads.smk) with example.smk; changed default output target from multiqc_report.html to output.txt; introduced single copy_file rule.
Template Configuration and Data {{ project_name }}/data/config.yaml.jinja, {{ project_name }}/data/input.txt	Added templated config with max_cores and sdm variables plus default_resources; created sample input.txt data file with placeholder content.
Template Documentation {{ project_name }}/.gitignore, {{ project_name }}/README.md.jinja, {{ project_name }}/config/README.md	Added standard Python/ML project ignore rules; refactored README header to use templated project_name and updated parameter documentation; removed workflow catalog badges and outdated references.

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~25 minutes

Possibly related PRs

• feat: larger update to feature fully-functional example and github actions #13: Directly reverses many changes in this PR by removing/undoing the Snakefile includes, workflow rules (common.smk, process_reads.smk), schemas, envs, and validate_fasta script additions.

Suggested reviewers

• dlaehnemann

Poem

🐰 A template renewed, so simple and clean,
Complex workflows trimmed to a minimal scene,
Copier guides future projects with care,
From intricate rules to examples so fair,
Now templates bloom bright in the workflow air! ✨

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment

📝 Coding Plan for PR comments

• Generate coding plan

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