chore: remove legacy Nextflow workflow files

[gregorweiss]

Closes #28

Remove the legacy workflows/ directory (5 Nextflow pipeline files) and a stale Nextflow comment in source code. These are fully superseded by Parsl-based orchestration.

Implementation plan posted as a comment below.

[gregorweiss]

Implementation Plan

Analysis

The workflows/ directory contains 5 Nextflow pipeline files from the initial commit (13d72c8). They are dead code — fully superseded by mdfactory/orchestration/ and the mdfactory build/mdfactory simulate CLI. One stale comment in mdfactory/analysis/submit.py also references Nextflow as a backend.

No runtime code, CI, tests, docs, or packaging references these files. Removal is a safe deletion with zero breakage risk.

Deliverables

1. Delete workflows/ directory (5 files):

   • workflows/build.nf
   • workflows/simulate.nf
   • workflows/nextflow.config
   • workflows/simulate.config
   • workflows/run_full_pipeline.sh

2. Update stale comment in mdfactory/analysis/submit.py:19:

   • Change: every SLURM-facing backend (submitit, Parsl, Nextflow) can share them.
   • To: every SLURM-facing backend (submitit, Parsl) can share them.

Files to modify

File	Change
workflows/build.nf	Delete
workflows/simulate.nf	Delete
workflows/nextflow.config	Delete
workflows/simulate.config	Delete
workflows/run_full_pipeline.sh	Delete
mdfactory/analysis/submit.py	Remove "Nextflow" from comment on line 19

Testing approach

• git grep -ri nextflow returns zero results (excluding .claude/ and .dreb/)
• pixi run -e dev test passes (existing tests unaffected)
• Docs build passes (no references to workflows/)

Acceptance criteria

• workflows/ directory removed
• Comment in submit.py updated
• Zero Nextflow references in repo (git grep)
• Tests pass
• Docs build passes

Risks

None. This is a pure deletion of unused files.

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Plan created by mach6

[gregorweiss]

Progress Update

Deleted the workflows/ directory containing 5 legacy Nextflow pipeline files (318 lines removed):

• workflows/build.nf
• workflows/simulate.nf
• workflows/nextflow.config
• workflows/simulate.config
• workflows/run_full_pipeline.sh

Tests pass (2483 passed, 1 pre-existing unrelated failure in test_lock_folder_processes).

Note: The submit.py comment mentioning Nextflow (from the issue) does not exist on main — it was introduced on feat/parsl-simulate and will be handled there separately.

Commit: 05d59d8

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Progress tracked by mach6

[gregorweiss]

Code Review

Important

Finding 1 — Docs still reference deleted workflows/ files on main (confidence: 97)
After this PR merges, docs/content/ and README.md still contain 20+ Nextflow references including runnable commands pointing to the now-deleted workflows/build.nf and workflows/simulate.nf. The issue acceptance criterion "git grep -ri nextflow returns zero results" is not met by this PR alone.

However: these doc references are already cleaned up by PR 27 which targets feat/parsl-simulate. When that branch merges to main, zero Nextflow references will remain. The question is sequencing — should this PR also update docs, or is the criterion met collectively across PR 27 + PR 29?

Strengths

• The 5 file deletions are correct and safe — zero Python imports reference workflows/
• CI does not reference the deleted files
• Tests pass (pre-existing unrelated failure only)
• Docs build passes (pages reference deleted files but build doesn't break)

Agents run: code-reviewer, completeness-checker

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Reviewed by mach6

[gregorweiss]

Review Assessment

#29 (comment)

Classifications

Finding	Classification	Reasoning
1: Docs still reference deleted workflows/	Deferred	Factual: True — 20+ Nextflow references remain in docs/README on main. Scope: The plan for this PR explicitly lists only file deletion + submit.py comment. The docs cleanup is already implemented in PR 27 (targeting feat/parsl-simulate). When that branch merges to main, zero Nextflow references will remain. This PR's scope is the source-code-level removal; duplicating PR 27's docs work here would create merge conflicts.

Action Plan

No genuine issues — the PR is safe to merge as-is. The "zero grep results" criterion will be satisfied when feat/parsl-simulate (which includes PR 27's docs changes) merges to main.

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Assessment by mach6