feat: complete minimal workflow as template

[m-jahn]

• added wf with 5 modules
• complete process of reading reads to processing to QC
• no local data; test data is generated on the fly

Summary by CodeRabbit

• New Features

  • Introduced new configuration files for managing genomic data processing and analysis.
  • Added multiple rules for processing genomic data, including fetching genomes, simulating reads, and generating quality reports.
  • Implemented a script for downloading and validating genome sequences and annotations from NCBI.

• Documentation

  • Updated README with detailed usage instructions and a structured table of contents.

• Chores

  • Enhanced GitHub Actions workflows for improved pull request validation and environment management.

[coderabbitai]

Caution

Review failed

The pull request is closed.

Walkthrough

The pull request includes significant updates across multiple workflow files and configurations. Key changes involve renaming workflow components, enhancing pull request validation processes, and introducing new configuration files for genomic data processing. The .gitignore file has been updated, and several new Conda environment configurations have been added for tools like Cutadapt and FastQC. Additionally, a new Snakefile structure has been established to facilitate genomic data processing, featuring rules for genome retrieval, read simulation, quality control, and reporting.

Changes

File	Change Summary
.github/workflows/conventional-prs.yml	Workflow name changed to "Lint PR", job renamed to "main", new step "Validate PR title" added, action version updated to v5, and permissions added for pull requests.
.github/workflows/main.yml	Branch triggers updated to include dev, added conditions to prevent execution by the github-actions[bot], upgraded actions/checkout to v4, and updated snakemake action versions.
.github/workflows/release-please.yml	Minor formatting change with no functional impact.
.gitignore	Added entry to ignore .test/results/*.
.test/config/config.yml	New configuration file added for genomic data processing with multiple sections for parameters and settings.
.test/config/multiqc_config.yml	Added remove_sections key to exclude samtools-stats from reports.
README.md	Updated Snakemake version requirement, modified GitHub Actions badge, added new badges, structured table of contents, and expanded sections for clarity.
config/config.yml	New configuration file added with settings for genomic analysis and read simulation.
config/multiqc_config.yml	Added remove_sections configuration option.
config/schemas/config.schema.yml	New JSON schema added for validating sample sheet entries with defined properties.
config/schemas/samples.schema.yml	New JSON schema added for sample sheet structure with required properties.
workflow/Snakefile	Added configuration loading, user feedback mechanisms, and minor formatting adjustments.
workflow/envs/cutadapt.yml	New Conda environment configuration for Cutadapt tool.
workflow/envs/fastqc.yml	New Conda environment configuration for FastQC tool.
workflow/envs/get_genome.yml	New Conda environment configuration for genomic data processing tools.
workflow/envs/multiqc.yml	New Conda environment configuration for MultiQC tool.
workflow/envs/simulate_reads.yml	New Conda environment configuration for read simulation.
workflow/rules/common.smk	New file for reading and validating sample sheets and configuration files.
workflow/rules/process_reads.smk	New workflow file defining rules for genomic data processing including genome retrieval and quality control.
workflow/scripts/get_genome.py	New script for downloading and validating genome sequence and annotation files from NCBI.

Poem

🐰 In the meadow where changes bloom,
New workflows dance, dispelling gloom.
With genomic tools, we hop and play,
Validating paths, come what may!
From samples to reports, we’ll find our way,
In this rabbit's world, it’s a bright new day! 🌼

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[m-jahn]

sorry, this was opened on the wrong repo!
My apologies.