Generate sequence structure mapping files for any organism #53
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Too chirpy. Run `snakefmt workflow/rules/*`
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I am a little confused. This PR seems to only have recent changes that I have already merged into main. |
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@jayhesselberth hmm.. okay im not sure what went wrong. let me retry |
Closes #40 * Set file extension * Eliminate input_format option
And reorganize rule files and summary outputs
Always build from source. The linux dist doesn't run on bodhi because glibc is out of date.
And snakefmt
Removing it causes it to fail.
TODO: compute these values directly from the BAM file.
Co-authored-by: Claude <noreply@anthropic.com>
* Add comprehensive CI/CD build and test checks This commit implements a complete testing and continuous integration infrastructure for the aa-tRNA-seq-pipeline: New CI/CD Components: - GitHub Actions CI workflow (.github/workflows/ci.yml) - Snakemake syntax validation with dry-run - Pipeline integration testing (merge_pods rule) - Configuration file validation - Automated tool setup (dorado, modkit) - GitHub Actions Lint workflow (.github/workflows/lint.yml) - Snakemake formatting checks (snakefmt) - Python code quality checks (black, flake8) - Markdown linting - YAML linting - Pre-commit hooks configuration (.pre-commit-config.yaml) - Automatic code quality checks before commits - Python formatting and linting - Snakemake formatting - General file hygiene checks - Local test script (.tests/run_local_tests.sh) - Quick validation script for local development - Checks Snakemake installation and syntax - Validates configuration files - Verifies directory structure Documentation: - Comprehensive testing guide (.github/TESTING.md) - CI/CD workflow documentation - Local testing instructions - Troubleshooting guide - Contributing guidelines - Updated README with CI status badges The CI workflow runs on all pushes and pull requests to main branches and claude/** branches. GPU-intensive rules are not tested in CI due to runner limitations but can be tested locally or on HPC clusters. * Fix CI workflow by replacing deprecated Mambaforge with Miniforge3 The Mambaforge variant is no longer available (404 error), causing the Snakemake Syntax Check to fail. Updated to use Miniforge3 as recommended by the setup-miniconda action warning. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com> --------- Co-authored-by: Claude <noreply@anthropic.com> Co-authored-by: lkwhite <laura.k.white@cuanschutz.edu>
This completes the test and build check infrastructure by adding: - SessionStart hook that automatically sets up the conda environment - Validates Snakemake installation and config files - Installs pre-commit hooks if not present - Runs quick syntax checks on session start - Comprehensive documentation in .claude/SETUP.md The hook ensures developers have a properly configured environment before starting work, reducing setup friction and catching issues early. Co-authored-by: Claude <noreply@anthropic.com>
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test data is charged sequencing data from T4 infection of WT E. coli.
test.py adds the charged adapter sequence to the 5' or 3' end of each sequence. This needs to be fixed since we use 'charged' and 'uncharged' adapters that have different 3' sequences.
The input is a converted .sto file (esl-reformat sto -> afa) containing conserved secondary structure across tRNAs, including phage. The reference sequence is used to create a mapping of sequence to structure position that can be used to correct nanopore sequence space position to structural position.