test: migrate test_bismark_tags.sh from cargo-from-SHA holodeck to pixi-pinned holodeck

[nh13]

Context

PR #89 ("ci: migrate parity tests from dwgsim/phiX174 to holodeck/chr22") established the canonical holodeck install path for this repo: test/holodeck/pixi.toml pinned to bioconda holodeck==0.2.1, invoked from CI via pixi run --frozen --manifest-path test/holodeck/pixi.toml -- holodeck ….

PR #90 ("feat(meth): emit Bismark-compatible XR/XG/XM auxiliary tags") added test/meth/test_bismark_tags.sh, a Layer-3 golden-truth diff against a holodeck-simulated bisulfite BAM. That test pins a different holodeck — SHA d240816c8c2dfbd72bdb3386679d0ad4d4f223e6 on branch nh/bisulfite-conversion, built via cargo build --release from a /tmp/holodeck-<sha> cache.

Why two install paths today

The nh/bisulfite-conversion branch (fg-labs/holodeck#11) adds --methylation-mode em-seq and the Bismark-compatible golden BAM emission that test_bismark_tags.sh exercises. fg-labs/holodeck#11 is open / not merged, so v0.2.1 (the bioconda release pinned by PR #89's pixi env) does not yet expose those flags. There is no released holodeck version that supports both the chr22-parity flow PR #89 uses and the bisulfite-chemistry flow PR #90's Layer-3 test needs, so PR #90 had to roll its own cargo-from-SHA install.

Migration to do once upstream lands

1. feat: split methylate from simulate; methylation truth via VCF MT/MB holodeck#11 merges to main.
2. A holodeck release containing methylation chemistry ships on bioconda (likely 0.3.0).
3. In test/holodeck/pixi.toml, bump holodeck = "==0.2.1" → the new version, refresh pixi.lock.
4. In test/meth/test_bismark_tags.sh:
   • Remove HOLODECK_SHA, HOLODECK_REPO, HOLODECK_DIR, HOLODECK_BIN, the cargo guard, and the clone/build block.
   • Replace direct "$HOLODECK_BIN" simulate … with pixi run --frozen --manifest-path "$HERE/../holodeck/pixi.toml" -- holodeck simulate … (same pattern PR ci: migrate parity tests from dwgsim/phiX174 to holodeck/chr22 #89's CI uses).
   • Drop the command -v cargo SKIP gate — pixi becomes the prerequisite instead.
5. CI: the existing Setup holodeck (pixi) step PR ci: migrate parity tests from dwgsim/phiX174 to holodeck/chr22 #89 added is reusable; the bismark test just needs to run on a matrix row that has the pixi env installed.

References

• PR ci: migrate parity tests from dwgsim/phiX174 to holodeck/chr22 #89 establishing pixi-based holodeck: ci: migrate parity tests from dwgsim/phiX174 to holodeck/chr22 #89
• PR feat(meth): emit Bismark-compatible XR/XG/XM auxiliary tags #90 introducing the cargo-from-SHA install: feat(meth): emit Bismark-compatible XR/XG/XM auxiliary tags #90
• Upstream blocker: feat: split methylate from simulate; methylation truth via VCF MT/MB holodeck#11