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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
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Summary
count-variants-sc(sc = scATAC only)Test plan
count-variants-sc --help— BED/Peak onlycount-variants --help— GTF still present🤖 Generated with Claude Code