feat: add ANNOTATE_HLAHD module - #260
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Post-processes HLA-HD class I output (final.result.txt + per-locus est.txt) into a P-group-annotated TSV, with an optional self-contained HTML report (pass --skip_html via task.ext.args to omit it). - Container: ghcr.io/mskcc-omics-workflows/hlahd-tools:1.0.0 (companion PR: mskcc-omics-workflows/containers#85) - Script vendored from mskcc/HLA_HD_workflow's scripts/annotate_hlahd.py + scripts/hlahd_annotate/ into resources/usr/bin/ (private repo, so it can't be pulled at container-build time -- same pattern as neoantigen-utils-base before neoantigen-utils had its own repo) - Test data: mskcc-omics-workflows/test-datasets@feature/annotate_hlahd (synthetic fixtures; pending Review Team promotion to an official 'annotate_hlahd' branch) - Tests: real-data run, --skip_html run (asserts the report output is empty), and stub -- all passing locally against the built image
The hlahd-tools:1.0.0 container now installs mskcc/hla-annotate (see companion containers PR) and exposes the 'annotate_hlahd' console script, so the module no longer needs to vendor a copy of the script under resources/usr/bin/. Re-verified: nf-test suite (real-data, --skip_html, stub) passes against the updated image -- identical output hashes to the vendored version.
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Summary
Adds
modules/msk/annotate_hlahd— post-processes HLA-HD class I output (<sample>_final.result.txt+ per-locus<sample>_{A,B,C}.est.txt) into a P-group-annotated TSV, with an optional self-contained HTML report.ghcr.io/mskcc-omics-workflows/hlahd-tools:1.0.0(companion PR: mskcc-omics-workflows/containers#85)[ meta, result_dir ],pgroup_filetsv(always),report(*_report.html, optional — pass--skip_htmlviatask.ext.argsto omit it),versionsOn the script
The actual annotation logic is mskcc/hla-annotate, installed by the
hlahd-toolscontainer (pinned tov1.0.0), which exposes anannotate_hlahdconsole command. It's also depended on directly by mskcc/HLA_HD_workflow (companion PR mskcc/HLA_HD_workflow#5 adds the--skip_htmlflag there) — one source of truth instead of vendoring copies into each consumer.Test data
Synthetic fixtures (not derived from any real sample) pushed to
test-datasets'feature/annotate_hlahdbranch — registered intests/config/test_data.config. Requesting Review Team promotion to an officialannotate_hlahdbranch.Verification
Ran locally against the
hlahd-tools:1.0.0image built from the companion containers PR (built forlinux/amd64, matchingtests/config/nf-test.config's--platform=linux/amd64):Checklist
feature/annotate_hlahd--skip_html, stub)versions.ymlemittedlabel(process_single) added