Release v1.4.0 by Jaureguy760 · Pull Request #88 · mcvickerlab/WASP2

Jaureguy760 · 2026-03-04T21:35:19Z

Summary

Update all 31 module container refs: biocontainers/wasp2:1.2.1 → ghcr.io/mcvickerlab/wasp2:1.4.0 (Docker + Singularity via GHCR)
Fix conf/test.config for all 4 pipelines (broken paths, remote URLs → local test data)
Fix samplesheet hardcoded absolute paths → ${projectDir} references
Add integration nf-test blocks (real data, no -stub) to all 4 pipelines (nf-rnaseq, nf-atacseq, nf-scatac, nf-outrider)
Add conda-lock.yml + environment.lock.yml for fully reproducible environments (mamba recommended)
Add AGENTS.md (velocity-bot config) and codecov.yml (coverage reporting)
nf-core compliance verified across all 4 pipelines

What's in this release

100 nf-tests passing (stub mode across all pipelines)
Rust-accelerated core (PyO3/maturin) with parity benchmarks vs Python WASP2 validated
Optimized multi-stage Dockerfile with cargo-chef caching
Bioconda PR #62972 open and all CI passing
Docker image published at ghcr.io/mcvickerlab/wasp2:1.4.0

Test plan

nf-test test tests/main.nf.test -profile test_stub,docker passes for all 4 pipelines
Integration tests runnable with -profile test,docker
docker pull ghcr.io/mcvickerlab/wasp2:1.4.0 succeeds
singularity pull wasp2.sif docker://ghcr.io/mcvickerlab/wasp2:1.4.0 succeeds
mamba create -n WASP2 --file conda-lock.yml resolves cleanly

🤖 Generated with Claude Code

Now that v1.4.0 is published on PyPI, add the real sha256 hash for the sdist tarball to the bioconda recipe. Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

Required by bioconda linter for downstream pinning. Pins to >=current,<next_major following semver. Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

CHANGELOG: - Add v1.4.0 entry documenting 14 bug fixes, pixi.toml, Python 3.13 support, and bioconda recipe bioconda recipe (fixes build failures on bioconda CI): - Fix cargo-bundle-licenses CLI (cd into rust/ instead of --manifest-path) - Remove --locked from maturin build (not supported in bioconda) - Add CARGO_TARGET_*_LINKER for conda C compiler - Use ${PYTHON} -m pip instead of bare pip - Add libdeflate to host (matches pysam build) - Make openssl conditional (not osx) - Skip py < 310 builds - Tighten typer to >=0.12.0 (match upstream) - Add pip check to test commands - Include THIRDPARTY.yml in license_file Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

- Skip Python 3.10 builds: bioconda's py310 packages use openssl 1.1.x which conflicts with htslib's openssl 3.x requirement - Add compiler('cxx') for libz-ng-sys Rust crate - Add cmake for libz-ng-sys build system - Update run python constraint to >=3.11 Users on Python 3.10 can still install from PyPI via pip. Co-Authored-By: Claude Opus 4.6 <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>

Copilot

Pull request overview

Release PR for WASP2 v1.4.0 that updates container references to GHCR, refreshes pipeline test data/config, and expands nf-test coverage (including “real data” integration tests) across the bundled Nextflow pipelines/modules.

Changes:

Update WASP2 container references across pipelines/modules to ghcr.io/mcvickerlab/wasp2:1.4.0 (Docker + Singularity via docker://).
Refresh and expand test fixtures (VCF/GTF/counts) + adjust sample naming/path handling to be ${projectDir}-relative.
Add/refresh nf-test suites and snapshots, including new integration test blocks for multiple pipelines.

Reviewed changes

Copilot reviewed 149 out of 166 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
tests/test_rust_python_counting_parity.py	Align test sample name with updated VCF header (lowercase).
tests/shared_data/variants.vcf	Update shared test VCF sample names + genotypes and expand variant set.
tests/shared_data/variants.vcf.gz	Add compressed VCF fixture for tests.
tests/shared_data/variants.vcf.gz.tbi	Add tabix index fixture for compressed VCF.
tests/shared_data/generate_core_data.sh	Update shared-data generator comments/VCF header for 3 lowercase samples.
tests/shared_data/expected_counts.tsv	Update expected output genotype delimiter formatting.
tests/shared_data/annotation.gtf	Expand shared GTF fixture (now covers additional genes).
pipelines/nf-scatac/tests/subworkflows/wasp_allelic_sc.nf.test	Remove old stub-only subworkflow tests.
pipelines/nf-scatac/tests/subworkflows/generate_fragments.nf.test.snap	Add new nf-test snapshot.
pipelines/nf-scatac/tests/modules/local/scatac_pseudobulk.nf.test.snap	Add new nf-test snapshot.
pipelines/nf-scatac/tests/modules/local/scatac_create_anndata.nf.test.snap	Add new nf-test snapshot.
pipelines/nf-scatac/tests/modules/local/scatac_count_alleles.nf.test.snap	Add new nf-test snapshot.
pipelines/nf-scatac/tests/modules/local/scatac_add_haplotype_layers.nf.test.snap	Add new nf-test snapshot.
pipelines/nf-scatac/tests/modules/local/scatac_count_alleles.nf.test	Update stub tests to use distinct NO_FILE sentinels.
pipelines/nf-scatac/tests/main.nf.test	Add integration nf-test block + update NO_FILE sentinels.
pipelines/nf-scatac/tests/data/samplesheet_test.csv	Add integration samplesheet fixture.
pipelines/nf-scatac/tests/data/samplesheet_local.csv	Replace hardcoded absolute paths with `${projectDir}`.
pipelines/nf-scatac/subworkflows/local/wasp_allelic_sc/main.nf	Harden BAM-branch detection against null/sentinel paths.
pipelines/nf-scatac/subworkflows/local/utils_nfscatac_pipeline.nf	Replace generic NO_FILE with typed NO_FILE_* sentinels in init.
pipelines/nf-scatac/nf-test.config	Run nf-tests with `test_stub,docker` profile by default.
pipelines/nf-scatac/nextflow.config	Add process container override to WASP2 1.4.0 + add `test_local` profile.
pipelines/nf-scatac/modules/local/scatac_pseudobulk/main.nf	Update module container to GHCR WASP2 1.4.0.
pipelines/nf-scatac/modules/local/scatac_create_anndata/main.nf	Update module container to GHCR WASP2 1.4.0.
pipelines/nf-scatac/modules/local/scatac_count_alleles/main.nf	Update module container + sentinel detection logic for optional filters.
pipelines/nf-scatac/modules/local/scatac_add_haplotype_layers/main.nf	Update module container + make stub output deterministic (seeded RNG).
pipelines/nf-scatac/conf/test_stub.config	Increase memory limit for stub tests.
pipelines/nf-scatac/conf/test_local.config	Add/adjust local test params and thresholds.
pipelines/nf-scatac/conf/test.config	Point `test` profile at local pre-generated test data.
pipelines/nf-rnaseq/tests/modules/local/wasp2_unified_make_reads.nf.test.snap	Add new nf-test snapshot.
pipelines/nf-rnaseq/tests/modules/local/wasp2_unified_make_reads.nf.test	Add real-data module test for unified make-reads.
pipelines/nf-rnaseq/tests/modules/local/wasp2_ml_output.nf.test.snap	Add new nf-test snapshot.
pipelines/nf-rnaseq/tests/modules/local/wasp2_filter_remapped.nf.test.snap	Add new nf-test snapshot.
pipelines/nf-rnaseq/tests/modules/local/wasp2_count_alleles.nf.test.snap	Add new nf-test snapshot.
pipelines/nf-rnaseq/tests/modules/local/wasp2_count_alleles.nf.test	Add real-data module test for counting.
pipelines/nf-rnaseq/tests/modules/local/wasp2_analyze_imbalance.nf.test.snap	Add new nf-test snapshot.
pipelines/nf-rnaseq/tests/modules/local/wasp2_analyze_imbalance.nf.test	Add real-data module test for imbalance analysis.
pipelines/nf-rnaseq/tests/modules/local/star_align.nf.test.snap	Add/refresh nf-test snapshots for STAR alignment stubs.
pipelines/nf-rnaseq/tests/main.nf.test.snap	Add snapshot for stub workflow task list.
pipelines/nf-rnaseq/tests/integration.nf.test	Simplify integration assertions to directory-level checks.
pipelines/nf-rnaseq/tests/data/test_snps.vcf.gz	Add compressed VCF fixture for tests.
pipelines/nf-rnaseq/tests/data/test_snps.vcf.gz.tbi	Add index fixture for compressed VCF.
pipelines/nf-rnaseq/tests/data/integration/integration.vcf.gz	Add compressed VCF fixture for integration tests.
pipelines/nf-rnaseq/tests/data/integration/integration.vcf.gz.tbi	Add index fixture for integration VCF.
pipelines/nf-rnaseq/nf-test.config	Default nf-test profile to `test_stub,docker` and adjust workDir handling.
pipelines/nf-rnaseq/nextflow.config	Add container overrides (WASP2 + STAR) and tweak docker profile.
pipelines/nf-rnaseq/modules/local/wasp2_unified_make_reads/main.nf	Update container + harden output renaming/validation logic.
pipelines/nf-rnaseq/modules/local/wasp2_ml_output/main.nf	Update module container to GHCR WASP2 1.4.0.
pipelines/nf-rnaseq/modules/local/wasp2_filter_remapped/main.nf	Update module container to GHCR WASP2 1.4.0.
pipelines/nf-rnaseq/modules/local/wasp2_count_alleles/main.nf	Update module container to GHCR WASP2 1.4.0.
pipelines/nf-rnaseq/modules/local/wasp2_analyze_imbalance/main.nf	Update module container to GHCR WASP2 1.4.0.
pipelines/nf-rnaseq/main.nf	Add `${projectDir}`/relative path resolver; stop passing GTF into count step (v1.4.0 note).
pipelines/nf-rnaseq/conf/test.config	Switch test profile to integration mini-genome dataset + lower thresholds.
pipelines/nf-rnaseq/conf/modules.config	Adjust publish patterns for filter stats output extension change.
pipelines/nf-outrider/workflows/outrider.nf	Adjust reference channels, add `outrider_min_count`, and emit multiqc placeholder.
pipelines/nf-outrider/tests/stub/samplesheet.csv	Fix stub samplesheet paths to be pipeline-relative.
pipelines/nf-outrider/tests/stub/variant_counts.tsv	Add stub fixture for variant counts.
pipelines/nf-outrider/tests/stub/allele_counts.tsv	Add stub fixture for allele counts.
pipelines/nf-outrider/tests/stub/count_matrix.tsv	Add stub fixture for merged count matrix.
pipelines/nf-outrider/tests/stub/sample1.gene_counts.tsv	Add stub fixture for gene counts.
pipelines/nf-outrider/tests/stub/sample2.gene_counts.tsv	Add stub fixture for gene counts.
pipelines/nf-outrider/tests/stub/sample3.gene_counts.tsv	Add stub fixture for gene counts.
pipelines/nf-outrider/tests/modules/local/outrider_fit.nf.test	Fix module script paths and align test inputs with stub data locations.
pipelines/nf-outrider/tests/modules/local/merge_counts.nf.test	Fix module script paths and align test inputs with stub data locations.
pipelines/nf-outrider/tests/modules/local/mae_detect.nf.test	Fix module script paths and align test inputs with stub data locations.
pipelines/nf-outrider/tests/modules/local/aggregate_counts.nf.test	Fix module script paths and align test inputs with stub data locations.
pipelines/nf-outrider/tests/main.nf.test	Rework pipeline tests: stub runs, required-input failures, and add integration run.
pipelines/nf-outrider/tests/data/samplesheet_test.csv	Replace hardcoded absolute paths with `${projectDir}`.
pipelines/nf-outrider/subworkflows/local/utils_nfoutrider_pipeline/main.nf	Add `${projectDir}`/relative path resolver and simplify completion logging.
pipelines/nf-outrider/nf-test.config	Run nf-tests with `test_stub,docker` profile by default.
pipelines/nf-outrider/nextflow.config	Add `outrider_min_count`, add `test_local`, and add container overrides.
pipelines/nf-outrider/modules/local/outrider_fit/main.nf	Update OUTRIDER version/container, add `min_count` input, and inline R logic.
pipelines/nf-outrider/modules/local/merge_counts/main.nf	Update module container to GHCR WASP2 1.4.0.
pipelines/nf-outrider/modules/local/mae_detect/main.nf	Update module container to GHCR WASP2 1.4.0.
pipelines/nf-outrider/modules/local/aggregate_counts/main.nf	Update module container and improve GTF bin indexing logic.
pipelines/nf-outrider/conf/test_local.config	Adjust local test params for expanded fixture set.
pipelines/nf-outrider/conf/test.config	Point test profile at local pre-generated test data; relax iterations/samples.
pipelines/nf-modules/tests/integration/benchmark_test.nf	Add an integration benchmark workflow for WASP2 modules.
pipelines/nf-modules/tests/data/test_counts.tsv	Add counts fixture for module real-data tests.
pipelines/nf-modules/tests/data/sample.vcf.gz	Add compressed sample VCF fixture.
pipelines/nf-modules/tests/data/sample.vcf.gz.tbi	Add index fixture for sample VCF.
pipelines/nf-modules/tests/data/minimal_keep.bam	Add minimal BAM fixture for filter-remapped tests.
pipelines/nf-modules/subworkflows/local/fastq_align_bwa/tests/main.nf.test.snap	Add/refresh nf-test snapshots.
pipelines/nf-modules/subworkflows/local/bam_stats_samtools/tests/main.nf.test.snap	Add/refresh nf-test snapshots.
pipelines/nf-modules/subworkflows/local/bam_stats_samtools/tests/main.nf.test	Adjust reference input shape for tests.
pipelines/nf-modules/subworkflows/local/bam_sort_stats_samtools/tests/main.nf.test	Adjust reference input shape for tests.
pipelines/nf-modules/nextflow.config	Centralize WASP2 v1.4.0 container refs and override containers for test execution.
pipelines/nf-modules/modules/wasp2/vcf_to_bed/main.nf	Update implementation for WASP2 v1.4.0 API and deduplicate outputs.
pipelines/nf-modules/modules/wasp2/vcf_to_bed/tests/main.nf.test.snap	Add snapshot updates for vcf_to_bed.
pipelines/nf-modules/modules/wasp2/unified_make_reads/main.nf	Update container + harden output renaming/validation logic.
pipelines/nf-modules/modules/wasp2/unified_make_reads/tests/main.nf.test	Add real-data module test coverage.
pipelines/nf-modules/modules/wasp2/unified_make_reads/tests/main.nf.test.snap	Add/refresh snapshot.
pipelines/nf-modules/modules/wasp2/ml_output/main.nf	Update container + write versions.yml from Python for robustness.
pipelines/nf-modules/modules/wasp2/ml_output/tests/main.nf.test	Convert tests to stub mode and simplify output assertions.
pipelines/nf-modules/modules/wasp2/map/main.nf	Update containers for map sub-processes.
pipelines/nf-modules/modules/wasp2/map/tests/make_reads.nf.test	Add real + stub tests for map make-reads.
pipelines/nf-modules/modules/wasp2/map/tests/make_reads.nf.test.snap	Add snapshot for map make-reads.
pipelines/nf-modules/modules/wasp2/map/tests/main.nf.test	Update filter test to use minimal_keep fixture.
pipelines/nf-modules/modules/wasp2/map/tests/main.nf.test.snap	Add snapshot for map tests.
pipelines/nf-modules/modules/wasp2/filter_remapped/main.nf	Update container and adjust CLI invocation semantics.
pipelines/nf-modules/modules/wasp2/filter_remapped/tests/main.nf.test	Add real-data test + adjust stub fixtures.
pipelines/nf-modules/modules/wasp2/filter_remapped/tests/main.nf.test.snap	Add snapshot updates.
pipelines/nf-modules/modules/wasp2/count_sc/main.nf	Update container and make stub output deterministic.
pipelines/nf-modules/modules/wasp2/count_sc/tests/main.nf.test	Update NO_FILE sentinels in tests.
pipelines/nf-modules/modules/wasp2/count_sc/tests/main.nf.test.snap	Add snapshot updates.
pipelines/nf-modules/modules/wasp2/count_alleles/main.nf	Update container to GHCR WASP2 1.4.0.
pipelines/nf-modules/modules/wasp2/count_alleles/tests/main.nf.test	Add real-data module test.
pipelines/nf-modules/modules/wasp2/count_alleles/tests/main.nf.test.snap	Add snapshot updates.
pipelines/nf-modules/modules/wasp2/count/main.nf	Update container to GHCR WASP2 1.4.0.
pipelines/nf-modules/modules/wasp2/count/tests/main.nf.test	Add real-data module test.
pipelines/nf-modules/modules/wasp2/count/tests/main.nf.test.snap	Add snapshot updates.
pipelines/nf-modules/modules/wasp2/analyze_imbalance/main.nf	Update container to GHCR WASP2 1.4.0.
pipelines/nf-modules/modules/wasp2/analyze_imbalance/tests/main.nf.test	Add real-data module test.
pipelines/nf-modules/modules/wasp2/analyze_imbalance/tests/main.nf.test.snap	Update snapshot meta and content.
pipelines/nf-modules/modules/wasp2/analyze/main.nf	Update container to GHCR WASP2 1.4.0.
pipelines/nf-modules/modules/wasp2/analyze/tests/min_count.config	Add test config to lower min_count for small fixtures.
pipelines/nf-modules/modules/wasp2/analyze/tests/main.nf.test	Add real-data test case.
pipelines/nf-modules/modules/wasp2/analyze/tests/main.nf.test.snap	Update snapshots.
pipelines/nf-atacseq/tests/subworkflows/nf-core/fastq_align_bwa/main.nf.test	Swap test inputs to local fixtures; simplify assertions.
pipelines/nf-atacseq/tests/subworkflows/nf-core/fastq_align_bowtie2/main.nf.test	Swap test inputs to local fixtures; simplify assertions.
pipelines/nf-atacseq/tests/subworkflows/nf-core/bam_stats_samtools/main.nf.test	Swap test inputs to local fixtures; simplify assertions.
pipelines/nf-atacseq/tests/subworkflows/nf-core/bam_markduplicates_picard/main.nf.test	Swap test inputs to local fixtures; simplify assertions.
pipelines/nf-atacseq/tests/subworkflows/local/prepare_genome/main.nf.test	Point tests at local reference fixtures.
pipelines/nf-atacseq/tests/modules/local/wasp2_make_reads.nf.test	Add real-data test and update stub fixtures/paths.
pipelines/nf-atacseq/tests/modules/local/wasp2_find_imbalance.nf.test	Add real-data test and update stub fixtures/paths.
pipelines/nf-atacseq/tests/modules/local/wasp2_filter_remapped.nf.test	Update stub fixture paths and simplify assertions.
pipelines/nf-atacseq/tests/modules/local/wasp2_count_variants.nf.test	Add real-data test and update stub fixtures/paths.
pipelines/nf-atacseq/tests/main.nf.test	Switch stub option to `-stub`, add integration test, adjust failure test.
pipelines/nf-atacseq/tests/data/stub_wasp_data.json	Add stub JSON fixture.
pipelines/nf-atacseq/tests/data/stub_counts.tsv	Add stub counts fixture.
pipelines/nf-atacseq/tests/data/samplesheet_test.csv	Replace hardcoded absolute paths with `${projectDir}` and lowercase sample_name.
pipelines/nf-atacseq/tests/data/samplesheet_local.csv	Add local samplesheet fixture.
pipelines/nf-atacseq/subworkflows/local/utils_nfattacseq_pipeline.nf	Add `${projectDir}`/relative path resolver + simplify completion logging.
pipelines/nf-atacseq/nf-test.config	Default nf-test profile to `test_stub,docker`.
pipelines/nf-atacseq/nextflow.config	Add `test_stub`/`test_local` profiles and set container overrides.
pipelines/nf-atacseq/modules/local/wasp2_make_reads/main.nf	Update container + harden output renaming/validation logic.
pipelines/nf-atacseq/modules/local/wasp2_make_reads.nf	Update container reference.
pipelines/nf-atacseq/modules/local/wasp2_find_imbalance/main.nf	Add preprocessing for WASP2 v1.4.0 count format compatibility; update container.
pipelines/nf-atacseq/modules/local/wasp2_find_imbalance.nf	Update container reference.
pipelines/nf-atacseq/modules/local/wasp2_filter_remapped/main.nf	Update container reference.
pipelines/nf-atacseq/modules/local/wasp2_filter_remapped.nf	Update container reference.
pipelines/nf-atacseq/modules/local/wasp2_count_variants/main.nf	Update container reference.
pipelines/nf-atacseq/modules/local/wasp2_count_variants.nf	Update container reference.
pipelines/nf-atacseq/conf/test_stub.config	Add stub test profile with local fixtures + container override.
pipelines/nf-atacseq/conf/test_local.config	Update local test config to use local fixtures/indices.
pipelines/nf-atacseq/conf/test.config	Switch `test` profile to local fixtures (no remote URLs).
pipelines/nf-atacseq/conf/modules.config	Remove/adjust some publishDir blocks for test context.
environment.lock.yml	Add pinned conda-lock source-of-truth environment spec.
codecov.yml	Add Codecov configuration (informational thresholds, ignores, flags).
bioconda-recipe/meta.yaml	Update bioconda recipe for WASP2 1.4.0 (Rust build + deps + license files).
bioconda-recipe/build.sh	Adjust maturin build steps and cross-platform build environment setup.
README.md	Update install docs for Bioconda/Docker/Singularity/conda-lock; add badge.
Dockerfile	Introduce cargo-chef caching + BuildKit cache mounts; update build/runtime stages.
CHANGELOG.md	Add v1.4.0 release notes entry.
AGENTS.md	Add velocity-bot guardrails/config doc.
.gitignore	Ignore additional nf-test output directories.
.dockerignore	Keep `tests/shared_data/` and a smoke-test script in build context; refine ignores.

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Copilot · 2026-03-04T21:52:14Z

pipelines/nf-scatac/modules/local/scatac_count_alleles/main.nf

+    def filter_barcodes = !barcodes.name.startsWith('NO_FILE') ? "true" : "false"
+    def filter_peaks = !peaks.name.startsWith('NO_FILE') ? "true" : "false"


SCATAC_COUNT_ALLELES uses sentinel filenames (NO_FILE_*) to decide whether to apply barcode/peak filtering, but barcodes and peaks are declared as required path inputs. In real (non-stub) runs, passing file('NO_FILE_BARCODES') / file('NO_FILE_PEAKS') will be staged as inputs and will fail if those files do not exist. Prefer making these inputs truly optional (path(barcodes), optional: true and path(peaks), optional: true) and adjusting the logic to handle null/empty inputs instead of relying on non-existent placeholder files.

Copilot · 2026-03-04T21:52:15Z

pipelines/nf-modules/modules/wasp2/count_sc/main.nf

    def sample = meta.sample?.toString()?.replaceAll(/[^a-zA-Z0-9._-]/, '_') ?: ''
    def sample_arg = sample ? "-s ${sample}" : ''
-    def feature_arg = features.name != 'NO_FILE' ? "-f ${features}" : ''
+    def feature_arg = !features.name.startsWith('NO_FILE') ? "-f ${features}" : ''


features is treated as optional via a NO_FILE* sentinel, but it is declared as a required path(features) input. In non-stub executions this will error when the sentinel path doesn't exist. Make features an optional input (optional: true) and update the feature_arg logic to check for a null/empty value instead of a fake filename.

Copilot · 2026-03-04T21:52:15Z

pipelines/nf-atacseq/conf/test_stub.config

+// Override ALL process containers for stub testing (only needs bash)
+process {
+    withName: '.*' {
+        container = 'ghcr.io/mcvickerlab/wasp2:1.4.0'
+    }
+}


This stub profile overrides the container for all processes (withName: '.*'). That will also override containers for alignment/QC steps (e.g., BWA/SAMTOOLS) during non-stub runs such as the integration nf-test in this PR, and the WASP2 image does not necessarily contain those tools. Scope this override to only the processes that are actually run in stub mode (or remove it and rely on the per-process container definitions in nextflow.config).

Suggested change

// Override ALL process containers for stub testing (only needs bash)

process {

withName: '.*' {

container = 'ghcr.io/mcvickerlab/wasp2:1.4.0'

}

}

Copilot · 2026-03-04T21:52:15Z

tests/shared_data/generate_core_data.sh

+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample1	sample2	sample3
+chr_test	750	snp001	C	T	100	PASS	DP=50	GT:DP	0/1:50	0/1:50	0/1:50
+chr_test	1200	snp002	T	G	100	PASS	DP=50	GT:DP	0/1:50	0/1:50	0/1:50
+chr_test	2800	snp003	A	C	100	PASS	DP=50	GT:DP	0/1:50	0/1:50	0/0:50
+chr_test	3200	snp004	G	A	100	PASS	DP=50	GT:DP	0/1:50	0/0:50	0/0:50
+chr_test	5000	snp005	G	T	100	PASS	DP=50	GT:DP	0/1:50	0/1:50	0/1:50
+chr_test	10800	snp006	T	C	100	PASS	DP=50	GT:DP	0/1:50	0/1:50	0/0:50
+chr_test	11200	snp007	A	G	100	PASS	DP=50	GT:DP	0/1:50	0/1:50	0/1:50
+chr_test	12800	snp008	C	A	100	PASS	DP=50	GT:DP	0/1:50	0/0:50	0/0:50


generate_core_data.sh still emits unphased genotypes (0/1) in the generated VCF, but the committed tests/shared_data/variants.vcf and expected_counts.tsv now use phased | genotypes. Re-running this generator would recreate a VCF that doesn't match the checked-in fixtures; update the generator to output 0|1 / 0|0 etc to keep regeneration deterministic.

Copilot · 2026-03-04T21:52:16Z

pipelines/nf-modules/modules/wasp2/vcf_to_bed/main.nf

    def args = task.ext.args ?: ''
    def prefix = task.ext.prefix ?: "${meta.id}"
    def sample_arg = samples ? "--samples ${samples}" : ''
    """


sample_arg is computed but never used in the process script. Either remove it, or use it to drive samples_list generation (or pass samples via CLI if that's the intended interface) to avoid confusion about how sample filtering is controlled here.

Copilot · 2026-03-04T21:52:16Z

pipelines/nf-atacseq/nf-test.config

    workDir ".nf-test"
    configFile "nextflow.config"
-    profile "test"
+    profile "test_stub,docker"


nf-test.config sets the default profile to test_stub,docker, but this PR also adds a real-data integration test in tests/main.nf.test that does not select a different profile. As a result, the integration test will run under the stub profile (including container overrides from conf/test_stub.config), which is likely unintended. Consider switching the default nf-test profile back to test,docker (or set the integration test to explicitly use a non-stub profile).

Suggested change

profile "test_stub,docker"

profile "test,docker"

Jaureguy760 and others added 20 commits February 24, 2026 22:38

chore: add PyPI sha256 to bioconda recipe for v1.4.0 (#76)

05689a1

Now that v1.4.0 is published on PyPI, add the real sha256 hash for the sdist tarball to the bioconda recipe. Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

chore: add run_exports to bioconda recipe (#77)

42e5025

Required by bioconda linter for downstream pinning. Pins to >=current,<next_major following semver. Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

fix: also skip Python 3.13 in bioconda recipe

deca934

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>

fix: add LIBCLANG_PATH and clangdev for bindgen

d48a432

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>

fix: remove CLI verification from build.sh

caf77f4

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>

fix: set MACOSX_DEPLOYMENT_TARGET for conda wheel compat

4576d18

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

fix: hardcode MACOSX_DEPLOYMENT_TARGET=10.13 for wheel compat

a7d6c00

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.

fix: replace conda llvm-otool with system Xcode otool for macOS

3731cc4

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.

fix: remove additional-platforms from bioconda recipe

5dacb64

Sync with bioconda PR: ARM builds are opt-in, not required for merge. Will add ARM support in a follow-up PR.

Merge pull request #79 from mcvickerlab/fix/bioconda-skip-py310

99e41b4

fix: sync bioconda recipe with build fixes

Merge remote-tracking branch 'origin/master' into dev

983e0bf

Jaureguy760 requested a review from Copilot March 4, 2026 21:41

Jaureguy760 merged commit be0da80 into master Mar 4, 2026
9 of 15 checks passed

Copilot started reviewing on behalf of Jaureguy760 March 4, 2026 21:42 View session

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Release v1.4.0#88

Release v1.4.0#88
Jaureguy760 merged 20 commits intomasterfrom
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		def filter_barcodes = !barcodes.name.startsWith('NO_FILE') ? "true" : "false"
		def filter_peaks = !peaks.name.startsWith('NO_FILE') ? "true" : "false"

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