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MetaPathways 3.5.2: Nextflow local/Slurm workflows, PGDB builds and explorer - #8

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feat/nextflow-controller-db-build

Commits on Oct 2, 2026

Prepare MetaPathways 3.5.2 Nextflow workflows, reports and release testing
RyloByte
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04f6cb2
Simplify local and Slurm resource requests and job limits
RyloByte
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e4d677b
Add source-specific taxonomy and finish reviewer explorer validation
RyloByte
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a7778dd
Include taxonomy tests and reviewer audit in source packages
RyloByte
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02434a2
Remove misleading abundance and expected RNA import notices
RyloByte
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3c534f4
Make clean reviewer setup reproducible from the repository
RyloByte
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7b2822c
Align reviewer references with CAMI samples and handle zero-hit annotations
RyloByte
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9be84f1
Add opt-in per-sample compact results for complete workflows
RyloByte
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88fc7f2
Bound sample workflow wiring and large cleanup dependency fan-in
RyloByte
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07cc4a8
Remove obsolete wheel data directory and document clean HPC builds
RyloByte
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6df7d68
Report sample-specific workflow planning progress
RyloByte
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9db9cd5
Request one node explicitly for every Slurm task
RyloByte
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1c3cd2d
Lead user documentation with release installation routes and three-sample tests
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b958136
Present user guides as standard MetaPathways documentation
RyloByte
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313675a
Restore original MetaPathways abstract verbatim above quick start
RyloByte
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9d507e1
Simplify installation and reviewer quick start; bundle workflow helpers
RyloByte
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bba2f57
Lead complete workflow docs with Pathway Tools prerequisite
RyloByte
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9a790aa
Publish Markdown user guides with Sphinx and Mermaid on Read the Docs
RyloByte
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a6e72d6

Commits on Oct 3, 2026

Keep reviewer provenance versioned and credit CAMI throughout the guides
RyloByte
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9164e6d
Document detailed tool orchestration and verified workflow citations
RyloByte
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a320bb4
Prepare 3.5.2 draft PR and document dev-to-master promotion
RyloByte
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8805761
Adapt appnote workflow SVG and align documentation diagram styling
RyloByte
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c3e1df4
Center workflow title and clean PGDB connectors and figure notes
RyloByte
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1f0a050
Simplify workflow banner and legend layout
RyloByte
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123c8dc
Fix Mermaid connector contrast for dark GitHub backgrounds
RyloByte
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21ad1bd
Keep schema relationship labels legible on dark backgrounds
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9161e0f
Center workflow diagrams on a common documentation scale
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3abd534
Show primary MetaPathways workflow at full content width
RyloByte
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da26653
Expand homepage layout for readable primary workflow
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9302d6d
Reduce main workflow homepage side gutters
RyloByte
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79db63f
Give cropped main workflow a distinct image URL
RyloByte
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f0331b6
Keep compact PGDB builds in worker scratch and bundle diagnostics
RyloByte
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1f3bad5
Point documentation links to Hallam Lab MetaPathways site
RyloByte
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2937f33

Commits on Oct 4, 2026

Commits on Oct 5, 2026

Commits on Oct 7, 2026

Fix ORF hit counts and coordinate-based rRNA taxonomy parsing
RyloByte
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d37bcbc