Resistome / AMR (W4) transform suite + pipeline DAG render#11
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Resistome / AMR (W4) transform suite + pipeline DAG render#11phy0x1a79ed wants to merge 2 commits into
phy0x1a79ed wants to merge 2 commits into
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Encode Antonio's Resistome_Tony tool table as metasmith transforms over the already-published assemblies (contigs + Prodigal proteins + COMEBin MAGs), preserving the original k141_XXXXXX contig IDs end-to-end (never re-calling ORFs) so his master integration table merges cleanly. Added (24 transforms): - DIAMOND ARG/VF (clone of diamond_tcdb chunk+merge): megares, bacmet, vfdb - single biocontainer: rgi (+rgi_mag on COMEBin MAGs), amrfinderplus, integronfinder, instrain (BAM-limited to 12 gapfill samples), strainphlan (reuses metaphlan.oci), crassphage (reuses bbtools.oci) - BUILD-blocked (container recipes scaffolded in container_builds): pathofact, feast, mobileelementfinder - 8 DB downloaders incl. the missing downloadVirsorter2DB Reused as-is: genomad, virsorter2. Deduped: CoverM -> existing per-contig coverage + comebin contig_to_bin. New annotation/container data types + .oci refs. Verified: dev.sh -b builds clean; GenerateWorkflow task.ok=True for megares (orfs->chunk->merge) and rgi targets. Also fix dev.sh -b for the current `metasmith build` CLI (positional STEP + repeatable -t/-u/-r; the old multi-value glob leaked resources/lib into STEP). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Add downloadPathofactDB.py local stub (product annotation::pathofact_db, the one resistome input with no producer; points at Zenodo 14192463) so the planner can close the whole resistome graph. Add main/render_resistome_dag.py, which renders the pipeline as two complementary DAGs (results/, gitignored): the resistome annotation layer (13 terminal tools + DIAMOND chunk/merge fan-out + DB downloaders) and an upstream preprocessing companion (prodigal/comebin/metaphlan). Split because a single joint MCTS solve over all 13 diverse full-length branches does not converge; seeding the 4 coupling-heavy intermediates makes it tractable (~20s, deterministic at seed=1). Both pathofact_db and feast_sources resolve via local stubs for now — not runnable; real container builds + Antonio's reference data still pending. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Resistome / AMR (W4) transform suite + pipeline DAG render
Adds the full resistome tool suite for the Spanish Lakes W4 (AMR/resistome) workflow, encoded as metasmith transforms, plus a re-runnable DAG renderer. Rebased onto the current
spanish-lakes-metagenomicstip;_metadata/regenerated viametasmith buildso the union of these types and the upstream PathoLogic types is consistent and reproducible (verified: a clean rebuild produces no diff).Terminal tools (per Antonio's
Resistome_Tonyspec)rgi,rgi_magon COMEBin MAGs), AMRFinderPlus, MEGARes / BacMet / VFDB via DIAMOND (ORF-chunk fan-out →merge_*).All ARG/VF/MGE tools preserve the original
k141_XXXXXXcontig IDs for Antonio's downstream merge.Logistics (reference-DB downloaders)
downloadCardDB,downloadAmrfinderDB,downloadMegaresDB,downloadBacmetDB,downloadVfdbDB,downloadVirsorter2DB,downloadCrassphageRef, plus stub downloaders for the data/build-blocked inputs (downloadPathofactDB,downloadFeastSources) so the graph closes.Container resources
Adds
.ocipointers:rgi,amrfinderplus,integronfinder,instrain,mobileelementfinder,pathofact,feast.DAG render
main/render_resistome_dag.pyrenders the end-to-end resistome DAG (seeds the coupling-heavy intermediates so the multi-branch solve converges).Known stubs / deferred (not runnable as-is)
annotation::pathofact_db(Zenodo 14192463) +containers::pathofact.oci— build deferred.annotation::feast_sources(curated source matrix) +containers::feast.oci— data + build deferred.containers::mobileelementfinder.oci— no biocontainer yet.downloadMegaresDB—diamond makedb(protein) on the MEGARes nucleotide FASTA; needs a translate step.🤖 Generated with Claude Code