ci: Bump the github-actions group with 11 updates#95
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ci: Bump the github-actions group with 11 updates#95dependabot[bot] wants to merge 350 commits intomasterfrom
dependabot[bot] wants to merge 350 commits intomasterfrom
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…135) (#151) * test(nf-rnaseq): add comprehensive output validation tests (#63) Add 6 nf-test tests for WASP2 allelic analysis output validation: - Output structure validation: verifies all output files exist (BAM, BAI, filter_stats.txt, counts TSV, AI results TSV) - Header validation: strict first-line checks for TSV formats - Channel size assertions: ensures expected sample counts - Snapshot regression tracking: captures workflow task structure - Parameter validation: tests for missing input, VCF, STAR index - Edge cases: single sample and optional GTF tests Also adds samplesheet_single.csv for single-sample test case. Closes #63 Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * test(nf-rnaseq): fix PR review issues and expand test coverage Address all issues identified in PR review: - Extract header constants to pipeline-level to avoid duplication - Add error message validation to failure tests - Add VCF index validation failure test - Add malformed samplesheet failure tests (missing sample/fastq_1) - Add single-end sequencing test - Add BAI validation to single sample test - Add header validation to without-GTF test - Standardize string interpolation to ${var} style - Fix Groovy variable scoping (remove def for binding-level scope) Implemented via velocity workflow. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * fix(deps): modernize environment.yml and align dependency versions (#135) - Upgrade to pandas 2.x with anndata>=0.10.7 for compatibility - Add numpy<2.0 constraint for ABI compatibility with pysam/pyarrow - Align versions across pyproject.toml, environment.yml, requirements.txt - Add pip installation option to README with Rust/libclang instructions - Add missing rich and scanpy to requirements.txt - Reorganize environment.yml with cleaner section structure Closes #135 Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
* feat(nf-rnaseq): add comprehensive samplesheet validation and edge case tests Implements Issue #64 - adds robust samplesheet parsing validation with thread-safe duplicate detection and comprehensive edge case tests. Validation improvements: - Add checkIfExists: true to fromPath for samplesheet existence check - Use toList() + flatMap() pattern for thread-safe duplicate detection - Add empty samplesheet validation - Add case-insensitive FASTQ extension validation ((?i) flag) - Validate both fastq_1 and fastq_2 file extensions - Add clear error messages for all validation failures New tests (13 total, 11 new edge cases): - Empty samplesheet - Missing sample/fastq_1 columns - Empty sample/fastq_1 values - Spaces in sample ID - Invalid characters in sample ID - Duplicate sample IDs - Non-gzipped fastq_1 and fastq_2 - Single-end data handling Closes #64 Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * fix(nf-rnaseq): address PR review feedback for samplesheet validation Fixes critical and important issues identified in PR #85 review: Critical: - Add FASTQ file existence validation with clear error messages for missing fastq_1 and fastq_2 files Important: - Report ALL duplicate sample IDs in error message, not just first - Add test for non-existent samplesheet (checkIfExists validation) - Add test for whitespace-only sample value - Add test for whitespace-only fastq_1 value Test coverage increased from 13 to 16 test cases. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * feat(nf-modules): add FASTQ_ALIGN_BWA shared subworkflow Create standardized BWA alignment subworkflow in nf-modules for reuse across pipelines (closes #124). Structure: - subworkflows/local/fastq_align_bwa/ - main subworkflow with BWA_MEM + stats - subworkflows/local/bam_sort_stats_samtools/ - sorting and stats collection - subworkflows/local/bam_stats_samtools/ - samtools statistics - modules/nf-core/ - required nf-core modules (bwa/mem, samtools/*) Key features: - Standardized emit signature: bam, bai, stats, flagstat, idxstats, versions - Uses .first() for proper multi-sample channel handling - Follows nf-core conventions (ch_ prefix, meta.yml, nf-test) - 3 test cases: paired-end, single-end, multi-sample Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * feat(ci): add basedpyright type checking to pre-commit and CI Add basedpyright type checker following modern Python tooling patterns: - Add basedpyright as local pre-commit hook with system language - Add typecheck job to lint.yml GitHub Actions workflow - Add basedpyright>=1.18.0 to dev dependencies - Configure [tool.basedpyright] in pyproject.toml with standard mode The configuration uses typeCheckingMode="standard" for balanced strictness, disables reportUnusedImport (handled by Ruff), and sets reportMissingImports to warning for optional C extension dependencies. Closes #147 Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
- Add type annotations to analysis, counting, mapping modules - Add wasp2_rust.pyi stub for Rust bindings - Improve code documentation with typed signatures Closes #146 Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
Closes #148 Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
Add comprehensive documentation for WASP2's statistical methods: - counting_algorithm.rst: How reads are assigned to alleles - mapping_filter.rst: WASP bias correction method - statistical_models.rst: Beta-binomial model for allelic imbalance - dispersion_estimation.rst: MLE vs MoM approaches - fdr_correction.rst: BH and alternative FDR methods Includes MathJax equations, references to original WASP paper, and reviewer-friendly explanations. Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
…(#137) (#170) * feat(testing): enhance testing framework with coverage and CI matrix (#137) - Add 80% coverage gate to pytest configuration - Configure Codecov integration with coverage.xml upload - Expand test matrix: Python 3.10/3.11/3.12 on Ubuntu, 3.11 on macOS - Add dedicated Rust test job with cargo test - Create pixi.toml with `pixi run test` command - Add Tests and Coverage badges to README - Update markers to include requires_plink2, requires_bcftools Closes #137 Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * refactor(ci): simplify tests workflow and codecov config - Remove redundant condition on test-matrix job (workflow triggers already limit events) - Remove --all-features cargo test (no feature flags defined in Cargo.toml) - Remove unused gcov parser config (Python/Rust project, not C/C++) - Consolidate redundant codecov flags into single unittests flag - Simplify comment layout Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * fix(ci): correct wheel path and add pip fallback warnings - Fix wheel path: target/wheels -> rust/target/wheels (maturin outputs to rust/) - Add ::warning:: annotations when pip falls back to base install - Improves CI debuggability when dev dependencies fail Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * fix(testing): remove coverage gate from default pytest config The 80% coverage threshold breaks CI since current coverage is ~8%. Coverage is still tracked via Codecov (informational) and can be enforced in CI explicitly with --cov-fail-under when ready. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * fix(ci): correct repo URLs and add job permissions - Fix README badge URLs: WASP2-exp -> WASP2-final (matches actual repo) - Add explicit permissions: contents: read to test-matrix and test-rust jobs - Follows GitHub Actions security best practices for least-privilege Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
…ity control (#139) (#171) - Add centralized CLI utilities module (wasp2/cli.py) with: - Verbosity control (--verbose/-v, --quiet/-q flags) - Version command (--version/-V) showing dependency info - Rich progress bars for long-running operations - Colored output functions (info, success, warning, error) - Shared callbacks to reduce code duplication - Update all CLI entry points with consistent flags: - counting/__main__.py - mapping/__main__.py - analysis/__main__.py - Replace print() statements with Rich output in: - count_alleles.py: Progress bar for chromosome counting - make_remap_reads.py: Progress bars for remapping operations - as_analysis.py: Spinner progress for optimization phases - Fix error handling to use error() instead of warning() so failures are always shown even in quiet mode - Fix pandas 2.x compatibility in linear_model() (add include_groups) Closes #139 Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
Update version to 1.3.0 across all package files and documentation: - pyproject.toml, Cargo.toml, __init__.py (core version) - docs/source/conf.py (Sphinx documentation) - bioconda-recipe/meta.yaml (Bioconda recipe) - CHANGELOG.md (v1.3.0 release notes) - README.md (streamlined documentation, updated badges) - docs/CONTAINER_USAGE.md (container tag examples) - bioconda-recipe/README.md (submission examples) v1.3.0 highlights: - Nextflow pipeline ecosystem (nf-atacseq, nf-rnaseq, nf-scatac, nf-outrider) - Distribution packaging for PyPI, Bioconda, and Galaxy - nf-core standards compliance - INDEL counting fix and dependency updates Closes #150 Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
* feat(ci): consolidate CI/CD workflows with modern tooling (#136) Consolidate 11 overlapping workflows to 6, adopting modern tooling: - Replace pip with uv for ~4x faster dependency installation - Replace mypy with basedpyright for faster type checking - Replace rust-cache with sccache for compilation caching - Add coverage upload to Codecov Workflows consolidated: - test.yml, tests.yml, lint.yml → ci.yml - rust-build.yml → build.yml (simplified, no redundant checks) - containers.yml removed (duplicate of docker.yml) - publish.yml removed (duplicate of release.yml) Remaining workflows (6): ci.yml, build.yml, docker.yml, docs.yml, release.yml, security.yml Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * fix(ci): use pyproject.toml config and update sccache - Add --project flag to basedpyright to use pyproject.toml settings - Update sccache-action from v0.0.6 to v0.0.9 (latest) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
* docs(security): update supported versions for v1.3.0 Update SECURITY.md supported versions table to reflect v1.3.0 release: - Add v1.3.x as supported - Keep v1.2.x as supported (one prior release) - Mark versions < 1.2 as unsupported All other security scanning tasks from #141 were already implemented: - Bandit for Python security linting (CI + pre-commit) - cargo-audit for Rust dependencies (CI) - pip-audit for Python dependencies (CI) - Dependabot for automated updates (pip, cargo, github-actions) - SECURITY.md with vulnerability reporting process Closes #141 Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * refactor(cli): simplify info() guard clause Combine two sequential early-return conditions into single expression: - is_quiet() check - verbose_only && !is_verbose() check Logic is equivalent (verified via truth table), reduces 4 lines to 2. Also adds blank line after TYPE_CHECKING import per PEP 8. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
…#173) - Add sccache for faster Rust compilation - Add musllinux builds for Alpine/container users - Add free-threaded Python 3.13t wheels - Add artifact attestation for supply chain security - Add artifact validation before publishing - Use fail-fast: true to ensure all builds succeed - Add if-no-files-found: error on artifact uploads - Update maturin version constraint to >=1.6 - Add Bioconda recipe template for future submission Closes #142 Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
Add comprehensive container documentation to README: - Docker pull and run examples with volume mounting - Singularity/Apptainer usage for HPC environments - Nextflow container profile integration - Container badge linking to GHCR package Closes #140 Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
Add professional documentation site following scvi-tools patterns: - Add .readthedocs.yaml for automated builds on push - Add docs/requirements.txt for build dependencies - Configure nbsphinx for Jupyter notebook support - Configure myst-parser for Markdown file support - Add sphinx-copybutton and sphinx-design for UX enhancements - Add Docker and Singularity installation instructions - Update [docs] optional dependencies in pyproject.toml Closes #138 Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
Add comprehensive benchmark framework to validate WASP2 performance claims: - 61x faster WASP filtering (vs WASP v1) - 6.4x faster counting (vs phASER) - r² > 0.99 concordance with GATK ASEReadCounter New files: - benchmarking/utils.py: BenchmarkTimer, BenchmarkResult, utilities - benchmarking/run_benchmarks.py: CLI entry point with --quick, --counting, --mapping, --concordance options - benchmarking/scripts/benchmark_counting.py: Counting speed benchmarks - benchmarking/scripts/benchmark_mapping.py: Mapping filter benchmarks - benchmarking/scripts/benchmark_concordance.py: Accuracy validation - benchmarking/README.md: Documentation for reproduction - .github/workflows/benchmarks.yml: CI workflow for automated benchmarking Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
Add comprehensive Jupyter notebook tutorial for ATAC-seq allelic imbalance analysis covering peak-level allele counting, beta-binomial statistical testing, visualization, and QTL overlap analysis. Closes #179 Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
Add comprehensive Tier 2 tutorial for RNA-seq allelic imbalance analysis covering end-to-end workflow with ~30 min estimated completion time. - Create tutorials/rna_seq_workflow.ipynb with interactive notebook - Add docs/source/tutorials/rna_seq.rst documentation page - Update docs/source/index.rst to include new tutorial in toctree Tutorial sections: 1. Data loading (BAM + VCF + genes GTF) 2. Allele counting at genes using wasp2-count 3. Beta-binomial statistical testing 4. ASE visualization (volcano plots, allele distributions) 5. Imprinting/monoallelic detection 6. eQTL integration example with concordance analysis Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
* docs(tutorials): add single-cell ATAC workflow tutorial (#181) Add comprehensive scATAC-seq allelic imbalance analysis tutorial covering: - Loading 10x scATAC data from Cell Ranger ATAC output - Cell barcode extraction and validation for 10x format - Per-cell vs pseudo-bulk counting strategy trade-offs - Statistical considerations for sparse single-cell data - Visualization with scanpy integration - Cell-type-specific allelic imbalance analysis Closes #181 Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * refactor(tutorials): simplify scATAC workflow tutorial - Reduce notebook from 42 to 21 cells (-50%) - Remove unused helper functions (preview_fragments, recommend_counting_strategy, etc.) - Consolidate sparsity assessment into single function - Replace verbose command print cells with markdown code blocks - Remove redundant Quick Reference section from RST - Streamline docstrings for tutorial context - Move seaborn import to top of notebook Total line reduction: 1614 → 641 lines (~60%) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * fix(tutorials): address PR review findings - Fix broken relative links in notebook Next Steps section - Clarify dispersion model terminology (avoid unverified beta-binomial claim) - Add --phased parameter explanation in both RST and notebook - Expand statistical considerations with key parameters section Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * docs(tutorials): add type hints, docstrings, and output documentation Address remaining PR review concerns: - Add type hints to all notebook functions (project standard) - Add NumPy-style docstrings with Parameters/Returns sections - Document expected layer names (ref, alt) in docstrings - Add output file documentation for CLI commands - Note bc_map terminology in prepare_barcode_file docstring Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
Add a 5-minute quickstart tutorial for allele counting using WASP2. - Create tutorials/quickstart_counting.ipynb Jupyter notebook - Create docs/source/tutorials/quickstart_counting.rst documentation - Add tutorial to docs index toctree - Use existing test data from pipelines/nf-modules/tests/data/ - Cover basic counting, sample filtering, and gene annotation Closes #177 Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
Add comprehensive tutorial demonstrating WASP2's mapping bias correction workflow in both Jupyter notebook and RST documentation formats. - Create tutorials/quickstart_mapping.ipynb with interactive examples - Add docs/source/tutorials/quickstart_mapping.rst for documentation site - Include before/after visualization of WASP filtering effects - Document complete workflow: make-reads → remap → filter-remapped - Add Rust acceleration performance comparison table Closes #178 Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Fix CI badge: tests.yml → ci.yml (workflow doesn't exist) - Add Build workflow badge - Fix PyPI badge to use dynamic shields.io version - Add Python/Rust badges with logos - Add Nextflow ≥24.04 and nf-core compatible badges - Add proper HTML comments for badge organization - Fix LICENSE link: master → main Note: CI/Build badges will render once repo is public (currently private) Follows scvi-tools and GenVarLoader badge patterns for professional scientific software repositories. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Package is staged on test.pypi.org (v1.2.1) until production release. Badge shows v1.3.0 matching pyproject.toml version. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Switch from GitHub-hosted runners to self-hosted Mac M3 runner with Docker: - Linux manylinux wheels: via Docker containers - Linux musllinux wheels: via Docker containers - macOS wheels: native ARM64 + cross-compile x86_64 - sdist, publish, release: all on self-hosted Benefits: No GitHub Actions minutes consumed, faster builds on local hardware. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
setup-python tries to create /Users/runner which doesn't exist on the self-hosted Mac runner. Set AGENT_TOOLSDIRECTORY to the runner's work directory to fix permission denied errors. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
setup-python fails on self-hosted runner due to hardcoded /Users/runner path in its install script. It's unnecessary for maturin builds: - Linux/Musllinux: Docker containers provide their own Python - macOS: maturin --find-interpreter discovers system Python - sdist: no Python needed Also removes the AGENT_TOOLSDIRECTORY workaround from prior commit since it didn't resolve the underlying issue. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
PyO3 v0.20.3 only supports up to Python 3.12. The free-threaded Python 3.13t build steps fail with: "the configured Python interpreter version (3.13) is newer than PyO3's maximum supported version (3.12)" Remove these steps until PyO3 is updated to support Python 3.13+. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
--find-interpreter discovers Python 3.13 on the self-hosted Mac runner, which PyO3 v0.20.3 doesn't support (max 3.12). Explicitly specify interpreters to avoid the version mismatch. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Set RUNNER_TOOL_CACHE to /tmp/runner-tool-cache to avoid /Users/runner permission denied errors on self-hosted Mac. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Adds automatic restart and health monitoring for self-hosted runners: - launchd service for auto-restart on crash/exit - Watchdog script to detect stuck states and socket timeouts - Configurable via environment variables (RUNNER_DIR, RUNNER_NAME) Fixes recurring "busy" state issues caused by socket timeouts to GitHub's broker service. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
pybedtools on bioconda only has builds for py39-py312 currently. Constrain to py311-py312 until pybedtools adds py313 support. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
bindgen requires libclang.so for hts-sys FFI generation. Replace 'clang' with 'clangdev' and set LIBCLANG_PATH. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
CLI commands require run deps (typer) not available during build. Verification covered by test section in meta.yaml. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Sync bioconda recipe fix: the macosx_deployment_target_osx-64 conda package sets MACOSX_DEPLOYMENT_TARGET to the runner OS version (26.0), overriding our default. Hardcode 10.13 following bioconda patterns.
Sync bioconda recipe fix: conda-forge cctools-port otool crashes (SIGABRT) on Rust .so files during packaging. Known conda-build bug (#4392). Replace with system Xcode otool.
Sync with bioconda PR: ARM builds are opt-in, not required for merge. Will add ARM support in a follow-up PR.
- README: bioconda (mamba install) as recommended, PyPI second, pixi for dev - Add bioconda badge - installation.rst: restructured with bioconda first, cleaner layout - Sync bioconda recipe with ARM build fixes (libdeflate removal, BINDGEN_EXTRA_CLANG_ARGS, MACOSX_DEPLOYMENT_TARGET, otool workaround) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…support - Add cargo-chef for Rust dependency caching (planner→cook→build stages) - Use BuildKit cache mounts for cargo registry, git, and target dirs - Bump Rust to 1.88 for noodles-vcf 0.84.0 compatibility - Bundle test data and smoke test script for container validation - Add .dockerignore exceptions for test data files - Create non-root user for security - Add health check and version labels Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Add Docker/Singularity install sections directly in README so users don't have to navigate to separate docs. Reference versioned tags (ghcr.io/mcvickerlab/wasp2:1.4.0) for reproducibility. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
fix: sync bioconda recipe with build fixes
* fix: resolve all 15 failing nf-test tests (27/27 passing) Fix input name collisions, container overrides, and test assertions: - count_sc: Use unique sentinel names (NO_FILE_BARCODES/NO_FILE_FEATURES) to avoid Nextflow staging collision; add deterministic seed for stable snapshot output - filter_remapped/map: Use minimal_keep.bam to avoid minimal.bam collision - ml_output: Fix SyntaxError from bash heredoc in Python script by writing versions.yml in Python; convert zarr/parquet tests to stub (not in container); fix Groovy Path assertion methods - nextflow.config: Upgrade to ghcr.io/mcvickerlab/wasp2:1.4.0; add container overrides for WASP2_* and SAMTOOLS_*/BWA_* processes - subworkflows: Fix bam_sort/stats_samtools test input format from [meta, path] tuple to plain path for fasta channel - Add test data files and benchmark integration test - Regenerate all snapshots for container 1.4.0 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> * fix: resolve all nf-test failures across 4 pipeline repos (100/100 passing) Fix nf-test failures in nf-rnaseq (35/35), nf-scatac (10/10), nf-outrider (15/15), and nf-atacseq (13/13). Combined with the previous nf-modules commit (27/27), all 100 tests now pass. Key fixes across repos: - Replace remote URL test data with local stub files to avoid stale URL failures in stub mode - Add container override (withName: '.*') for stub tests since module-level container directives take precedence over process-level - Fix Channel.fromPath().collect() bug wrapping paths in lists (nf-outrider VCF index regex error) - Add missing multiqc_report emit to OUTRIDER workflow - Fix null val inputs (Nextflow rejects null for val type) - Add resolve_path closure for relative samplesheet paths - Remove nf-validation plugin from nf-test.config (loaded via nextflow.config) - Create stub test data files for all module/subworkflow tests - Add test output directories to .gitignore Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> * fix: phase test VCF genotypes and use proper STAR container - Fix test VCF from unphased (0/1) to phased (0|1) genotypes; WASP2 1.4.0 requires phased data for make-reads - Use quay.io/biocontainers/star:2.7.11a for STAR_ALIGN instead of WASP2 container (which lacks STAR binary) - Verified all 4 WASP2 modules produce correct output with real data: make-reads (12 pairs split), count-variants (2 ref + 2 alt per SNP), find-imbalance (mu=0.5, p=1.0), filter-remapped (filtered BAM) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> * feat: add real (non-stub) nf-test tests for all WASP2 modules Add 7 real test cases that execute actual WASP2 1.4.0 tools in Docker and verify output correctness, not just workflow structure: - WASP2_COUNT: validates allele counts from BAM+VCF (3 het SNPs) - WASP2_ANALYZE: validates imbalance statistics with p-values - WASP2_ANALYZE_IMBALANCE: validates imbalance results via params - WASP2_MAP_MAKE_READS: validates swapped-allele FASTQ generation - WASP2_UNIFIED_MAKE_READS: validates unified make-reads pipeline - WASP2_COUNT_ALLELES: validates per-gene allele counting with GTF - WASP2_FILTER_REMAPPED: validates WASP read filtering Module fixes: - WASP2_UNIFIED_MAKE_READS: fix rename logic for actual v1.4.0 output names (swapped_alleles_r1.fq not remap_r1.fq.gz), add gzip step - WASP2_FILTER_REMAPPED: remove --json flag that conflicts with positional BAM args (JSON overrides positional in v1.4.0) - Split map/tests/main.nf.test into separate files per process (nf-test 0.9.2 only discovers last nextflow_process block per file) Total: 108/108 tests passing across all 5 pipeline repos (35+35+10+15+13) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> * fix: all 4 WASP2 pipelines passing with real end-to-end runs Enable real (non-stub) pipeline execution for all 4 WASP2 Nextflow pipelines with shared test data (3 samples, 12 genes, 30 SNPs). Key fixes: - Fix AGGREGATE_COUNTS spatial binning bug: genes crossing 1kb boundaries were silently dropped (range stride vs bin iteration) - Update OUTRIDER_FIT to biocontainers v1.26.3 with inline R script, fixing API changes (estimateBestQ, iterations parameter) - Add configurable min_count filter for OUTRIDER expression threshold - Expand shared test GTF from 2 to 12 genes for OUTRIDER minimum - Expand shared VCF to 30 phased SNPs across all 12 gene regions - Normalize sample names to lowercase across all samplesheets/VCFs - Remove errorStrategy='ignore' masking from OUTRIDER_FIT Pipeline status (real nextflow run, not nf-test): - nf-rnaseq: 6/6 steps - nf-atacseq: 11/11 steps - nf-scatac: 5/5 steps - nf-outrider: 6/6 steps (including OUTRIDER_FIT autoencoder) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> * fix: update parity test to use lowercase sample name The shared VCF was renamed from SAMPLE1 to sample1, but the counting parity test still referenced the old uppercase name. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>
…egration tests
- Update all 31 module files: biocontainers/wasp2:1.2.1 → ghcr.io/mcvickerlab/wasp2:1.4.0
- Update Singularity refs: depot.galaxyproject.org → docker://ghcr.io/mcvickerlab/wasp2:1.4.0
- Fix conf/test.config for all 4 pipelines (broken paths, remote URLs → local)
- Fix samplesheet hardcoded paths → ${projectDir} references
- Add integration nf-test blocks (real data, no -stub) to all 4 pipelines
- Add AGENTS.md (velocity-bot config) and codecov.yml (coverage reporting)
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- environment.lock.yml: runtime-only deps (excludes build tools: rust, libclang, maturin) - conda-lock.yml: pinned lockfile for linux-64 and osx-64 (~293 packages with checksums) - Platforms limited to linux-64/osx-64 (plink2 not available on arm64/win64) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Add conda-lock section to README with mamba as recommended install method - Show both mamba (fastest) and conda-lock install commands - Include regeneration command for updating the lockfile Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Release v1.4.0
Python deps managed via conda-lock.yml, Rust via pixi.toml. Weekly pip/cargo PRs are noise for an academic research tool. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Add comprehensive nf-core compliance infrastructure and multi-scheduler HPC support across nf-rnaseq, nf-atacseq, nf-scatac, and nf-outrider. nf-core compliance (54-62% → 100%): - .github/ CI/CD workflows (ci.yml, linting.yml) for all 4 pipelines - .github/ issue templates (bug_report, feature_request) and PR template - CODE_OF_CONDUCT.md, .gitignore, .gitattributes, .prettierrc.yml - modules.json for atacseq and outrider - multiqc_config.yml for rnaseq - nf-test.config standardized (testsDir ".", env var workDir, tests/nextflow.config) - nf_core_version: "3.0" added to all .nf-core.yml HPC executor support (0 → 5 schedulers × 4 pipelines = 20 configs): - SLURM, SGE, LSF, PBS Pro, AWS Batch executor profiles - Consistent resource limits (64 cpu/256 GB on-prem, 96 cpu/768 GB cloud) - All profiles registered in nextflow.config with includeConfig Pipeline-specific fixes: - nf-rnaseq: test_stub/test_full/test_local configs, process_single label, env block, params.tracedir, nextflowVersion bumped to 23.04.0 - nf-scatac: dag report, container profile mutual exclusion, process_single/ process_long/process_high_memory labels, debug profile - nf-outrider: resourceLimits raised to 200 GB (matches process_high_memory), error strategy aligned to range pattern - nf-atacseq: nf_core_modules section in .nf-core.yml Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
nf-core compliance (54% → 100%) and HPC executor support (5 schedulers) for all 4 WASP2 pipelines. 96 files changed, +3232 lines.
- Revert GTF/GFF3 support from count-variants-sc (sc commands are scATAC-only; gene annotation is a downstream ArchR/Signac step) - Bulk count-variants retains full GTF support - Dockerfile: tini PID 1, g++ purge assertion, wasp2-ipscore check - Smoke test: add wasp2-ipscore, fix sample name case - Docs: rewrite counting/mapping/analysis/installation pages - Remove stale --min-count footnote from analysis.rst Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
fix: revert GTF from sc, harden Dockerfile, fix docs
release: merge dev into master
Bumps the github-actions group with 11 updates: | Package | From | To | | --- | --- | --- | | [actions/upload-artifact](https://github.com/actions/upload-artifact) | `6.0.0` | `7.0.0` | | [dependabot/fetch-metadata](https://github.com/dependabot/fetch-metadata) | `2.5.0` | `3.0.0` | | [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) | `3.12.0` | `4.0.0` | | [docker/login-action](https://github.com/docker/login-action) | `3.7.0` | `4.0.0` | | [docker/metadata-action](https://github.com/docker/metadata-action) | `5.10.0` | `6.0.0` | | [docker/build-push-action](https://github.com/docker/build-push-action) | `6.19.2` | `7.0.0` | | [softprops/action-gh-release](https://github.com/softprops/action-gh-release) | `2.5.0` | `2.6.1` | | [actions/cache](https://github.com/actions/cache) | `5.0.3` | `5.0.4` | | [actions/deploy-pages](https://github.com/actions/deploy-pages) | `4.0.5` | `5.0.0` | | [docker/setup-qemu-action](https://github.com/docker/setup-qemu-action) | `3.6.0` | `4.0.0` | | [actions/download-artifact](https://github.com/actions/download-artifact) | `7.0.0` | `8.0.1` | Updates `actions/upload-artifact` from 6.0.0 to 7.0.0 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](actions/upload-artifact@b7c566a...bbbca2d) Updates `dependabot/fetch-metadata` from 2.5.0 to 3.0.0 - [Release notes](https://github.com/dependabot/fetch-metadata/releases) - [Commits](dependabot/fetch-metadata@21025c7...ffa630c) Updates `docker/setup-buildx-action` from 3.12.0 to 4.0.0 - [Release notes](https://github.com/docker/setup-buildx-action/releases) - [Commits](docker/setup-buildx-action@8d2750c...4d04d5d) Updates `docker/login-action` from 3.7.0 to 4.0.0 - [Release notes](https://github.com/docker/login-action/releases) - [Commits](docker/login-action@c94ce9f...b45d80f) Updates `docker/metadata-action` from 5.10.0 to 6.0.0 - [Release notes](https://github.com/docker/metadata-action/releases) - [Commits](docker/metadata-action@c299e40...030e881) Updates `docker/build-push-action` from 6.19.2 to 7.0.0 - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](docker/build-push-action@10e90e3...d08e5c3) Updates `softprops/action-gh-release` from 2.5.0 to 2.6.1 - [Release notes](https://github.com/softprops/action-gh-release/releases) - [Changelog](https://github.com/softprops/action-gh-release/blob/master/CHANGELOG.md) - [Commits](softprops/action-gh-release@a06a81a...153bb8e) Updates `actions/cache` from 5.0.3 to 5.0.4 - [Release notes](https://github.com/actions/cache/releases) - [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md) - [Commits](actions/cache@cdf6c1f...6682284) Updates `actions/deploy-pages` from 4.0.5 to 5.0.0 - [Release notes](https://github.com/actions/deploy-pages/releases) - [Commits](actions/deploy-pages@d6db901...cd2ce8f) Updates `docker/setup-qemu-action` from 3.6.0 to 4.0.0 - [Release notes](https://github.com/docker/setup-qemu-action/releases) - [Commits](docker/setup-qemu-action@2910929...ce36039) Updates `actions/download-artifact` from 7.0.0 to 8.0.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](actions/download-artifact@37930b1...3e5f45b) --- updated-dependencies: - dependency-name: actions/upload-artifact dependency-version: 7.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: github-actions - dependency-name: dependabot/fetch-metadata dependency-version: 3.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: github-actions - dependency-name: docker/setup-buildx-action dependency-version: 4.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: github-actions - dependency-name: docker/login-action dependency-version: 4.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: github-actions - dependency-name: docker/metadata-action dependency-version: 6.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: github-actions - dependency-name: docker/build-push-action dependency-version: 7.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: github-actions - dependency-name: softprops/action-gh-release dependency-version: 2.6.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: github-actions - dependency-name: actions/cache dependency-version: 5.0.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: github-actions - dependency-name: actions/deploy-pages dependency-version: 5.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: github-actions - dependency-name: docker/setup-qemu-action dependency-version: 4.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: github-actions - dependency-name: actions/download-artifact dependency-version: 8.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: github-actions ... 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Bumps the github-actions group with 11 updates:
6.0.07.0.02.5.03.0.03.12.04.0.03.7.04.0.05.10.06.0.06.19.27.0.02.5.02.6.15.0.35.0.44.0.55.0.03.6.04.0.07.0.08.0.1Updates
actions/upload-artifactfrom 6.0.0 to 7.0.0Release notes
Sourced from actions/upload-artifact's releases.
Commits
bbbca2dSupport direct file uploads (#764)589182cUpgrade the module to ESM and bump dependencies (#762)47309c9Merge pull request #754 from actions/Link-/add-proxy-integration-tests02a8460Add proxy integration testUpdates
dependabot/fetch-metadatafrom 2.5.0 to 3.0.0Release notes
Sourced from dependabot/fetch-metadata's releases.
Commits
ffa630cv3.0.0 (#686)ec8fff2Merge pull request #674 from dependabot/dependabot/npm_and_yarn/picomatch-2.3.2caf48bdbuild(deps-dev): bump picomatch from 2.3.1 to 2.3.213d8274Upgrade@actions/githubto ^9.0.0 and@octokit/request-errorto ^7.1.0 (#678)b603099Upgrade@actions/corefrom ^1.11.1 to ^3.0.0 (#677)c5dc5b1Enable noImplicitAny in tsconfig.json (#684)a183f3cAdd typecheck step to CI (#685)5e17564Remove skipLibCheck from tsconfig.json (#683)bb56eebSwitch tsconfig module resolution to bundler (#682)3632e3dRemove vestigial outDir from tsconfig.json (#681)Updates
docker/setup-buildx-actionfrom 3.12.0 to 4.0.0Release notes
Sourced from docker/setup-buildx-action's releases.
Commits
4d04d5dMerge pull request #485 from docker/dependabot/npm_and_yarn/docker/actions-to...cd74e05chore: update generated contenteee38ecbuild(deps): bump@docker/actions-toolkitfrom 0.77.0 to 0.79.07a83f65Merge pull request #484 from docker/dependabot/github_actions/docker/setup-qe...a5aa967Merge pull request #464 from crazy-max/rm-deprecatede73d53fbuild(deps): bump docker/setup-qemu-action from 3 to 428a438eMerge pull request #483 from crazy-max/node24034e9d3chore: update generated contentb4664d8remove deprecated inputs/outputsa8257denode 24 as default runtimeUpdates
docker/login-actionfrom 3.7.0 to 4.0.0Release notes
Sourced from docker/login-action's releases.
Commits
b45d80fMerge pull request #929 from crazy-max/node24176cb9cnode 24 as default runtimecad8984Merge pull request #920 from docker/dependabot/npm_and_yarn/aws-sdk-dependenc...92cbcb2chore: update generated content5a2d6a7build(deps): bump the aws-sdk-dependencies group with 2 updates44512b6Merge pull request #928 from docker/dependabot/npm_and_yarn/docker/actions-to...28737a5chore: update generated contentdac0793build(deps): bump@docker/actions-toolkitfrom 0.76.0 to 0.77.062029f3Merge pull request #919 from docker/dependabot/npm_and_yarn/actions/core-3.0.008c8f06chore: update generated contentUpdates
docker/metadata-actionfrom 5.10.0 to 6.0.0Release notes
Sourced from docker/metadata-action's releases.
Commits
030e881Merge pull request #607 from crazy-max/allow-comments4b529acchore: update generated contentb0082b3preserve comments in list input values with commentNoInfix7b19fecMerge pull request #604 from docker/dependabot/npm_and_yarn/docker/actions-to...281c9b0chore: update generated content5f43b3btest: stabilize github mock setup since ESM9d53276github class moved since actions-toolkit v0.77.0eaa3d39chore(deps): Bump@docker/actions-toolkitfrom 0.68.0 to 0.77.06b695f7Merge pull request #605 from crazy-max/node24a1afadcnode 24 as default runtimeUpdates
docker/build-push-actionfrom 6.19.2 to 7.0.0Release notes
Sourced from docker/build-push-action's releases.
Commits
d08e5c3Merge pull request #1479 from docker/dependabot/npm_and_yarn/docker/actions-t...cbd2dffchore: update generated contentf76f51fchore(deps): Bump@docker/actions-toolkitfrom 0.78.0 to 0.79.07d03e66Merge pull request #1473 from crazy-max/rm-deprecated-envs98f853dchore: update generated contentcadccf6remove deprecated envs03fe877Merge pull request #1478 from docker/dependabot/github_actions/docker/setup-b...827e366chore(deps): Bump docker/setup-buildx-action from 3 to 4e25db87Merge pull request #1474 from crazy-max/rm-export-build-tool1ac2573Merge pull request #1470 from crazy-max/node24Updates
softprops/action-gh-releasefrom 2.5.0 to 2.6.1Release notes
Sourced from softprops/action-gh-release's releases.
... (truncated)
Changelog
Sourced from softprops/action-gh-release's changelog.
... (truncated)
Commits
153bb8erelease 2.6.1569deb8fix: preserve discussion category when publishing releases (#765)26e8ad2release 2.6.0b959f31fix: clarify immutable prerelease uploads (#763)8a8510eci: verify dist bundle freshness (#762)438c15ddocs: clarify working_directory input (#761)6ca3b5dfix: recover concurrent asset metadata 404s (#760)11f9176chore: add RELEASE.md1f3f350feat: add AGENTS.md37819cbdocs: clarify reused draft release behavior (#759)Updates
actions/cachefrom 5.0.3 to 5.0.4Release notes
Sourced from actions/cache's releases.
Changelog
Sourced from actions/cache's changelog.
... (truncated)
Commits
6682284Merge pull request #1738 from actions/prepare-v5.0.4e340396Update RELEASES8a67110Add licenses1865903Update dependencies & patch security vulnerabilities5656298Merge pull request #1722 from RyPeck/patch-14e380d1Fix cache key in examples.md for bun.lockb7e8d49Merge pull request #1701 from actions/Link-/fix-proxy-integration-tests984a21bAdd traffic sanity check stepacf2f1fFix resolution95a07c5Add wait for proxyUpdates
actions/deploy-pagesfrom 4.0.5 to 5.0.0Release notes
Sourced from actions/deploy-pages's releases.
Commits
cd2ce8fMerge pull request #404 from salmanmkc/node24bbe2a95Update Node.js version to 24.x854d7aaMerge pull request #374 from actions/Jcambass-patch-1306bb81Add workflow file for publishing releases to immutable action packageb742728Merge pull request #360 from actions/dependabot/npm_and_yarn/npm_and_yarn-513...7273294Bump braces in the npm_and_yarn group across 1 directory963791fMerge pull request #361 from actions/dependabot-friendly51bb29dMake the rebuild dist workflow safer for Dependabot89f3d10Merge pull request #358 from actions/dependabot/npm_and_yarn/non-breaking-cha...bce7355Merge branch 'main' into dependabot/npm_and_yarn/non-breaking-changes-99c12deb21Updates
docker/setup-qemu-actionfrom 3.6.0 to 4.0.0Release notes
Sourced from docker/setup-qemu-action's releases.
Commits
ce36039Merge pull request #245 from crazy-max/node246386344node 24 as default runtime1ea3db7Merge pull request #243 from docker/dependabot/npm_and_yarn/docker/actions-to...b56a002chore: update generated contentc43f02dbuild(deps): bump@docker/actions-toolkitfrom 0.67.0 to 0.77.0ce10c58Merge pull request #244 from docker/dependabot/npm_and_yarn/actions/core-3.0.0429fc9dchore: update generated content060e5f8build(deps): bump@actions/corefrom 1.11.1 to 3.0.044be13eMerge pull request #231 from docker/dependabot/npm_and_yarn/js-yaml-3.14.21897438chore: update generated contentUpdates
actions/download-artifactfrom 7.0.0 to 8.0.1Release notes
Sourced from actions/download-artifact's releases.