plan_version: "1" source: kind: freeform name: "ΦX174 Planetary-Scale Retrospective DMS -- Workflow A (SRA Landscape & Spike-In Sieve)" derived_from: intent notes: >- Synthesized from freeform-summary.md (Stages A, B, C, D2), freeform-galaxy-interface.md (Workflow A section), freeform-galaxy-data-flow.md (nodes N1-N7), and iwc-comparison-notes.md (no High/Medium-confidence IWC domain exemplar found; kmindex and LexicMap do not appear anywhere in the IWC corpus). There is no upstream test-evidence (nf-test snapshot, CWL job file) for this project to translate -- every test case and assertion below is synthesized from stated workflow intent, the paper's own Table 1 / am3-diagnostic numbers, and the concrete workflow's declared step contracts. Grounded additionally against galaxy-workflow.gxwf.yml (the concrete 9-step gxformat2 draft) and test-data-refs.json (phase 7's gene E/J scoping decision and documented fixture gaps), per this run's explicit instruction to use them for consistency even though they are not this skill's own declared inputs. workflow: title: "phix174_sra_landscape_spikein_sieve (ΦX174 SRA Landscape & Spike-In Sieve, Workflow A)" label_source: draft notes: >- All workflow_label values below are the literal input/output ids from galaxy-workflow.gxwf.yml's inputs:/outputs: blocks (e.g. gene_query_panel, gene_e_am3_quarantine_audit), not the interface brief's earlier proposed prose labels (e.g. "Gene E am3 quarantine audit"), which in places differ from what the concrete draft actually shipped. implement-galaxy-workflow-test should still re-confirm these against the live draft before finalizing, since this skill's own declared inputs are the earlier template-era briefs (see warnings[0]). test_cases: - id: kmindex_wiring_smoke_generic_fixtures doc: >- Structural/wiring smoke test for the kmindex containment-screen chain (combine_gene_panel_to_bulk_fasta -> kmindex_containment_screen -> kmindex_hit_concat -> kmindex_hit_dedup_max_score) and for lexicmap_search's multi-index-selection binding, using each pinned Tool Shed wrapper's own real upstream functional-test fixtures (generic, non-phiX174 sequences and indices) instead of phiX174 biology. This exists because no small, real, locally-buildable Logan-shard kmindex index or Logan-derived LexicMap domain index exists at any scale smaller than usegalaxy.org's production data (test-data-refs.json gaps "no-real-small-kmindex-logan-shard-subset" and "no-real-small-lexicmap-logan-index-subset"). This case proves the workflow's collection map-over, multi-select DB/index binding, and per-gene sensitivity-override wiring execute without error; it does NOT audit any biological content, including the Gene E am3 diagnostic (see test case gene_e_j_am3_diagnostic_synthetic_lexicmap_index for that). The workflow's mandatory element_identifier=="E" extraction in extract_gene_e_am3_audit means every test case, including this one, must still supply an "E"-identified gene_query_panel element, even though here it carries generic (non-phiX174) sequence content. derived_from: intent provenance: >- test-data-refs.json tool_level_structural_fixtures (kmindex_query test #6 "using register index"; lexicmap.xml tests #3/#4/#6); iwc-comparison-notes.md "Test issues" routing note. job_inputs: - workflow_label: gene_query_panel label_status: resolved description: >- 2-element sample_sheet reusing the workflow's mandatory E/J identifiers but populated with each pinned tool's own generic upstream test query sequences, not real phiX174 CDS -- element "E" holds tools-iuc kmindex's query1.fasta content (or lexicmap's lexicmap_query3.fasta content), element "J" a second generic sequence from the same fixture sets. Per-gene LexicMap sensitivity override columns left unset for both (not meaningful for generic sequences). collection_shape: sample_sheet datatype: fasta fixture: storage: remote-url location: >- https://raw.githubusercontent.com/galaxyproject/tools-iuc/main/tools/kmindex/test-data/query1.fasta ; https://raw.githubusercontent.com/galaxyproject/tools-iuc/main/tools/lexicmap/test-data/lexicmap_query3.fasta checksum: null provenance: >- tools-iuc kmindex_query.xml test #6 and lexicmap.xml tests #3/#4/#6, both already used for upstream CI; not phiX174 biology. - workflow_label: kmindex_db_selection label_status: resolved description: >- kmindex's own test-only "register" value, which expands (in the wrapper's own functional test) to a real 2-shard multi-select (index1, index2) against a synthetic repeat-sequence index bundled in tools-iuc's test-data. collection_shape: null datatype: null fixture: storage: unresolved location: null checksum: null provenance: >- Value "register" is confirmed only inside kmindex_query.xml's own functional test harness; whether a workflow-level Planemo test job can pass it through the same way is unconfirmed -- see unresolved[2]. - workflow_label: kmindex_zvalue label_status: resolved description: workflow default. collection_shape: null datatype: null fixture: {storage: null, location: "6", checksum: null, provenance: "galaxy-workflow.gxwf.yml default"} - workflow_label: kmindex_threshold label_status: resolved description: workflow default. collection_shape: null datatype: null fixture: {storage: null, location: "0.3", checksum: null, provenance: "galaxy-workflow.gxwf.yml default"} - workflow_label: kmindex_output_format label_status: resolved description: workflow default. collection_shape: null datatype: null fixture: {storage: null, location: "json", checksum: null, provenance: "galaxy-workflow.gxwf.yml default"} - workflow_label: kmindex_fast label_status: resolved description: workflow default. collection_shape: null datatype: null fixture: {storage: null, location: "false", checksum: null, provenance: "galaxy-workflow.gxwf.yml default"} - workflow_label: lexicmap_index_selection label_status: resolved description: >- LexicMap's own real 2-index test combination (db.lmi + db2.lmi), indexing two small real viral RefSeq assemblies (GCF_001502155.1, GCF_001502175.1) -- not phiX174 and not Logan-derived. collection_shape: null datatype: null fixture: storage: unresolved location: null checksum: null provenance: >- tools-iuc lexicmap.xml tests #3/#4/#6 combine db.lmi+db2.lmi; whether the exact data-table name is reachable from a workflow-level test job is unconfirmed -- see unresolved[2]. - workflow_label: lexicmap_top_n_genomes label_status: resolved description: workflow default. collection_shape: null datatype: null fixture: {storage: null, location: "0", checksum: null, provenance: "galaxy-workflow.gxwf.yml default"} - workflow_label: lexicmap_advanced_all label_status: resolved description: workflow default. collection_shape: null datatype: null fixture: {storage: null, location: "true", checksum: null, provenance: "galaxy-workflow.gxwf.yml default"} - workflow_label: tiling_qc_min_coverage label_status: resolved description: workflow default. collection_shape: null datatype: null fixture: {storage: null, location: "0.8", checksum: null, provenance: "galaxy-workflow.gxwf.yml default"} - workflow_label: tiling_qc_min_coverage_partial label_status: resolved description: workflow default. collection_shape: null datatype: null fixture: {storage: null, location: "0.5", checksum: null, provenance: "galaxy-workflow.gxwf.yml default"} - workflow_label: tiling_qc_min_pident label_status: resolved description: workflow default. collection_shape: null datatype: null fixture: {storage: null, location: "60", checksum: null, provenance: "galaxy-workflow.gxwf.yml default"} - workflow_label: tiling_qc_max_internal_stops label_status: resolved description: workflow default. collection_shape: null datatype: null fixture: {storage: null, location: "0", checksum: null, provenance: "galaxy-workflow.gxwf.yml default"} - workflow_label: tiling_qc_sample_cap label_status: resolved description: workflow default. collection_shape: null datatype: null fixture: {storage: null, location: "10", checksum: null, provenance: "galaxy-workflow.gxwf.yml default"} - workflow_label: tiling_qc_allow_frameshifts label_status: resolved description: >- Confirmed OFF/False by direct read of nekrut/disassembler's lexicmap_streamer.py argparse (store_true, no default=True). collection_shape: null datatype: null fixture: {storage: null, location: "false", checksum: null, provenance: "test-data-refs.json inputs (tiling_qc_allow_frameshifts)"} expected_outputs: - workflow_label: kmindex_accession_union label_status: resolved description: >- Deduplicated accession union across the kmindex "register" test shards. Existence-only: the underlying index has no phiX174 biological relationship, so only "the chain ran and produced non-empty output" is assertable. output_kind: dataset collection_shape: null assertion_intent: - family: has_size intent: "Output is non-empty (chain executed and produced a result)." expected_value: null tolerance: {kind: none, magnitude: null, rationale: "existence-only, no content relationship to phiX174"} element_identifier: null evidence: intent confidence: low - workflow_label: clean_full_length_cds_haplotypes label_status: resolved description: "Per-gene clean haplotype FASTA (sample_sheet). Existence-only per element." output_kind: collection collection_shape: sample_sheet assertion_intent: - {family: has_size, intent: "Non-empty output for gene E.", expected_value: null, tolerance: null, element_identifier: "E", evidence: intent, confidence: low} - {family: has_size, intent: "Non-empty output for gene J.", expected_value: null, tolerance: null, element_identifier: "J", evidence: intent, confidence: low} - workflow_label: clean_haplotype_counts label_status: resolved description: "Per-gene clean haplotype counts table. Existence-only per element." output_kind: collection collection_shape: sample_sheet assertion_intent: - {family: has_n_columns, intent: "Table has a plausible column count (schema smoke check).", expected_value: null, tolerance: null, element_identifier: "E", evidence: intent, confidence: low} - {family: has_n_columns, intent: "Table has a plausible column count (schema smoke check).", expected_value: null, tolerance: null, element_identifier: "J", evidence: intent, confidence: low} - workflow_label: flagged_accessions label_status: resolved description: "Per-gene flagged (QC-failed) sequences. Existence-only, not audited for content in this case." output_kind: collection collection_shape: sample_sheet assertion_intent: [] - workflow_label: flagged_audit_reasons label_status: resolved description: "Per-gene flagged.tsv. Existence-only in this case; see the other test case for the real am3 assertion." output_kind: collection collection_shape: sample_sheet assertion_intent: - {family: has_n_lines, intent: "At least a header line is present.", expected_value: null, tolerance: {kind: none, magnitude: null, rationale: "existence-only"}, element_identifier: "E", evidence: intent, confidence: low} - workflow_label: per_gene_ingestion_summary label_status: resolved description: "Per-gene summary.json. Stochastic/opaque given generic non-phiX174 input; existence-only per corpus convention for JSON of this kind." output_kind: collection collection_shape: sample_sheet assertion_intent: - {family: has_text, intent: "Output is well-formed JSON.", expected_value: "{", tolerance: null, element_identifier: "E", evidence: intent, confidence: low} - {family: has_text, intent: "Output is well-formed JSON.", expected_value: "{", tolerance: null, element_identifier: "J", evidence: intent, confidence: low} - workflow_label: ingestion_manifest_all_genes label_status: resolved description: "All-gene manifest table. Existence-only (2 data rows expected structurally, not content-checked)." output_kind: dataset collection_shape: null assertion_intent: - {family: has_n_lines, intent: "Header plus 2 gene rows (E, J).", expected_value: 3, tolerance: {kind: delta, magnitude: 1, rationale: "tolerate a trailing-newline off-by-one"}, element_identifier: null, evidence: intent, confidence: medium} - workflow_label: gene_e_am3_quarantine_audit label_status: resolved description: >- Gene E element of flagged_tsv. In THIS case the "E" element is generic test-fixture sequence, not real phiX174 gene E, so no am3 diagnostic content is expected -- existence-only. The meaningful, content-bearing am3 assertion is in the other test case. output_kind: dataset collection_shape: null assertion_intent: - family: has_size intent: "Output exists (extraction step resolved a real E element and did not error)." expected_value: null tolerance: {kind: none, magnitude: null, rationale: "existence-only; not phiX174 biology in this case"} element_identifier: null evidence: intent confidence: low - id: gene_e_j_am3_diagnostic_synthetic_lexicmap_index doc: >- Primary functional test for Workflow A's core scientific claim (the paper's Sanger am3 spike-in diagnostic, freeform-summary.md Stage D2: genome position nt587 G->A causes a premature TGG->TAG stop at Gene E codon 7, gpE_W7*). Exercises lexicmap_search -> lexicmap_streamer_tiling_qc -> {flatten_gene_summary_json_to_row -> join_gene_summary_rows_into_manifest} and -> extract_gene_e_am3_audit end-to-end using a small, purpose-built synthetic LexicMap domain index (construction deferred to implement-galaxy-workflow-test / a follow-on find-test-data pass; this plan specifies its required composition per Fixture.storage=generated-toy) seeded with real cds/E.fasta and cds/J.fasta content plus 3 hand-crafted decoy accessions: (1) a Gene-E wildtype-clean decoy, (2) a Gene-E am3-positive decoy carrying the exact nt587 G->A / codon-7 TGG->TAG substitution, and (3) a Gene-J clean decoy. This is the smallest fixture that can produce a real, assertable Gene E am3 quarantine audit without waiting on usegalaxy.org-hosted production Logan indices (test-data-refs.json gap "no-real-completed-lexicmap-hits-table-for-lexicmap-streamer"). The kmindex chain shares the same job (one workflow invocation runs both chains) but is not the focus here and is only weakly asserted; see omissions[1]. derived_from: intent provenance: >- freeform-summary.md Stage D2 (am3 diagnostic: nt587 G->A, gpE_W7*, 2,215,172/2,392,457 = 92.59% of evaluated Gene E accessions); test-data-refs.json inputs[0] (real cds/E.fasta, cds/J.fasta, per-gene sensitivity overrides) and gaps[2]; galaxy-workflow.gxwf.yml extract_gene_e_am3_audit doc (flagged_tsv columns: accession, coverage, mean_pident, flag, n_stops, stop_codons, hsps_merged). job_inputs: - workflow_label: gene_query_panel label_status: resolved description: >- 2-element sample_sheet: E = real cds/E.fasta (273 bp CDS) with per-gene LexicMap sensitivity override columns populated (align_min_match_pident=60.0, align_min_match_len=35, seed_min_prefix=15, min_qcov_per_genome=30.0, sourced from logan_remaining_runs.json per test-data-refs.json); J = real cds/J.fasta (114 bp CDS, shortest gene in the panel), override columns unset (falls back to wrapper defaults 70/50/17/unset). collection_shape: sample_sheet datatype: fasta fixture: storage: in-repo location: "cds/E.fasta, cds/J.fasta" checksum: null provenance: >- test-data-refs.json inputs[0]; real files already used by this project's own kmindex/LexicMap submission scripts (submit_kmindex_all_genes.py, submit_remaining_logan.py). - workflow_label: kmindex_db_selection label_status: resolved description: "Real Logan shard names, kept only for job completeness; not this case's focus." collection_shape: null datatype: null fixture: storage: unresolved location: "GENOMIC_PHG,GENOMIC_VRL,METAGENOMIC_ENV" checksum: null provenance: >- test-data-refs.json kmindex_db_selection (real shard names, no backing test-scale index -- see unresolved[0]). - workflow_label: kmindex_zvalue label_status: resolved description: workflow default. collection_shape: null datatype: null fixture: {storage: null, location: "6", checksum: null, provenance: "galaxy-workflow.gxwf.yml default"} - workflow_label: kmindex_threshold label_status: resolved description: workflow default. collection_shape: null datatype: null fixture: {storage: null, location: "0.3", checksum: null, provenance: "galaxy-workflow.gxwf.yml default"} - workflow_label: kmindex_output_format label_status: resolved description: workflow default. collection_shape: null datatype: null fixture: {storage: null, location: "json", checksum: null, provenance: "galaxy-workflow.gxwf.yml default"} - workflow_label: kmindex_fast label_status: resolved description: workflow default. collection_shape: null datatype: null fixture: {storage: null, location: "false", checksum: null, provenance: "galaxy-workflow.gxwf.yml default"} - workflow_label: lexicmap_index_selection label_status: assumed description: >- Placeholder data-table name for the not-yet-built synthetic 3-decoy index described in this test case's doc (e.g. "PhiX174E_J_Am3ToyIndex"); real value to be assigned once the index is constructed. collection_shape: null datatype: null fixture: storage: generated-toy location: null checksum: null provenance: >- This plan specifies the index's required composition (wildtype-clean Gene E decoy, am3-positive Gene E decoy, clean Gene J decoy); construction is deferred -- see unresolved[1]. - workflow_label: lexicmap_top_n_genomes label_status: resolved description: workflow default. collection_shape: null datatype: null fixture: {storage: null, location: "0", checksum: null, provenance: "galaxy-workflow.gxwf.yml default"} - workflow_label: lexicmap_advanced_all label_status: resolved description: workflow default. collection_shape: null datatype: null fixture: {storage: null, location: "true", checksum: null, provenance: "galaxy-workflow.gxwf.yml default"} - workflow_label: tiling_qc_min_coverage label_status: resolved description: workflow default. collection_shape: null datatype: null fixture: {storage: null, location: "0.8", checksum: null, provenance: "galaxy-workflow.gxwf.yml default"} - workflow_label: tiling_qc_min_coverage_partial label_status: resolved description: workflow default. collection_shape: null datatype: null fixture: {storage: null, location: "0.5", checksum: null, provenance: "galaxy-workflow.gxwf.yml default"} - workflow_label: tiling_qc_min_pident label_status: resolved description: workflow default. collection_shape: null datatype: null fixture: {storage: null, location: "60", checksum: null, provenance: "galaxy-workflow.gxwf.yml default"} - workflow_label: tiling_qc_max_internal_stops label_status: resolved description: >- workflow default; 0 tolerated internal stops for the CLEAN cohort is exactly what routes the am3-positive decoy to the FLAGGED cohort instead. collection_shape: null datatype: null fixture: {storage: null, location: "0", checksum: null, provenance: "galaxy-workflow.gxwf.yml default"} - workflow_label: tiling_qc_sample_cap label_status: resolved description: workflow default. collection_shape: null datatype: null fixture: {storage: null, location: "10", checksum: null, provenance: "galaxy-workflow.gxwf.yml default"} - workflow_label: tiling_qc_allow_frameshifts label_status: resolved description: "Confirmed OFF/False from nekrut/disassembler's real argparse source." collection_shape: null datatype: null fixture: {storage: null, location: "false", checksum: null, provenance: "test-data-refs.json inputs (tiling_qc_allow_frameshifts)"} expected_outputs: - workflow_label: kmindex_accession_union label_status: resolved description: "Not this case's focus; see omissions[1]." output_kind: dataset collection_shape: null assertion_intent: [] - workflow_label: clean_full_length_cds_haplotypes label_status: resolved description: >- Per-gene clean haplotype FASTA. Gene E should contain exactly the wildtype-clean decoy (the am3-positive decoy is routed to FLAGGED, not here). Gene J should contain its one clean decoy. output_kind: collection collection_shape: sample_sheet assertion_intent: - family: has_text intent: "Gene E's clean cohort contains the wildtype-clean decoy accession, not the am3-positive one." expected_value: "E_wildtype_ctrl" tolerance: null element_identifier: "E" evidence: intent confidence: medium - family: has_text intent: "Gene J's clean cohort contains its clean decoy accession." expected_value: "J_clean_ctrl" tolerance: null element_identifier: "J" evidence: intent confidence: medium - workflow_label: clean_haplotype_counts label_status: resolved description: "Per-gene clean haplotype counts. Gene E: 1 clean haplotype. Gene J: 1 clean haplotype." output_kind: collection collection_shape: sample_sheet assertion_intent: - {family: has_n_lines, intent: "Header plus exactly 1 clean haplotype row for gene E.", expected_value: 2, tolerance: {kind: delta, magnitude: 1, rationale: "tolerate trailing-newline off-by-one"}, element_identifier: "E", evidence: intent, confidence: medium} - {family: has_n_lines, intent: "Header plus exactly 1 clean haplotype row for gene J.", expected_value: 2, tolerance: {kind: delta, magnitude: 1, rationale: "tolerate trailing-newline off-by-one"}, element_identifier: "J", evidence: intent, confidence: medium} - workflow_label: flagged_accessions label_status: resolved description: "Per-gene flagged (QC-failed) sequences. Gene E should contain exactly the am3-positive decoy. Gene J should be empty." output_kind: collection collection_shape: sample_sheet assertion_intent: - family: has_text intent: "Gene E's flagged cohort contains the am3-positive decoy accession." expected_value: "E_am3_ctrl" tolerance: null element_identifier: "E" evidence: intent confidence: medium - workflow_label: flagged_audit_reasons label_status: resolved description: >- Per-gene flagged.tsv (columns: accession, coverage, mean_pident, flag, n_stops, stop_codons, hsps_merged, per galaxy-workflow.gxwf.yml's confirmed real source read). This is the closest upstream signal to the am3 finding before extraction. output_kind: collection collection_shape: sample_sheet assertion_intent: - family: has_n_lines intent: "Gene E: header plus exactly 1 flagged row (the am3-positive decoy)." expected_value: 2 tolerance: {kind: delta, magnitude: 1, rationale: "tolerate trailing-newline off-by-one"} element_identifier: "E" evidence: intent confidence: medium - family: has_text intent: "Gene E's flagged row records the premature stop at codon 7, matching the paper's gpE_W7* diagnostic." expected_value: "7" tolerance: null element_identifier: "E" evidence: intent confidence: medium - family: has_n_lines intent: "Gene J: header only, no flagged accessions (clean decoy only)." expected_value: 1 tolerance: {kind: delta, magnitude: 0, rationale: "exact -- this fixture is fully controlled/deterministic by design"} element_identifier: "J" evidence: intent confidence: medium - workflow_label: per_gene_ingestion_summary label_status: resolved description: >- Per-gene summary.json. Deterministic here (tiny controlled fixture, not the stochastic/floating-point-heavy case the existence-only convention targets), so a surgical property assertion is used instead of "starts with {". output_kind: collection collection_shape: sample_sheet assertion_intent: - family: has_json_property_with_value intent: "Gene E evaluated exactly 2 accessions (wildtype-clean + am3-positive decoys)." expected_value: 2 tolerance: null element_identifier: "E" evidence: intent confidence: medium - family: has_json_property_with_value intent: "Gene E's cohort breakdown records exactly 1 premature-stop (am3-like) flagged accession." expected_value: 1 tolerance: null element_identifier: "E" evidence: intent confidence: medium - family: has_json_property_with_value intent: "Gene J evaluated exactly 1 accession (its one clean decoy)." expected_value: 1 tolerance: null element_identifier: "J" evidence: intent confidence: medium - workflow_label: ingestion_manifest_all_genes label_status: resolved description: "All-gene manifest table joining the E and J summary rows." output_kind: dataset collection_shape: null assertion_intent: - family: has_n_lines intent: "Header plus 2 gene rows (E, J)." expected_value: 3 tolerance: {kind: delta, magnitude: 1, rationale: "tolerate trailing-newline off-by-one"} element_identifier: null evidence: intent confidence: medium - family: has_text intent: "Manifest's first column is the gene symbol (per flatten_gene_summary_json_to_row's own confirmed column-1-is-gene contract)." expected_value: "gene" tolerance: null element_identifier: null evidence: intent confidence: medium - workflow_label: gene_e_am3_quarantine_audit label_status: resolved description: >- FLAGSHIP ASSERTION. Gene E element of flagged_tsv, extracted by extract_gene_e_am3_audit (__EXTRACT_DATASET__, by_identifier "E"). With this test case's synthetic index, this should contain exactly one row: the am3-positive decoy, flagged for a premature stop at codon 7 -- the workflow-level, assertable analog of the paper's real finding that 2,215,172/2,392,457 (92.59%) of evaluated Gene E accessions carry the nt587 G->A / gpE_W7* substitution. Real full-scale numbers are recorded only as directional context in test-data-refs.json and are NOT asserted here (see omissions[0]). output_kind: dataset collection_shape: null assertion_intent: - family: has_n_lines intent: "Exactly one flagged row (header plus the single am3-positive decoy) for the tiny controlled fixture." expected_value: 2 tolerance: {kind: delta, magnitude: 0, rationale: "exact -- this output is a direct extraction of a fully controlled synthetic fixture, not a stochastic tool result"} element_identifier: null evidence: intent confidence: medium - family: has_text intent: "The flagged row identifies the am3-positive decoy accession." expected_value: "E_am3_ctrl" tolerance: null element_identifier: null evidence: intent confidence: medium - family: has_text intent: "The flagged row's stop_codons column records position 7, matching the paper's Gene E codon-7 TGG->TAG (gpE_W7*) diagnostic mutation at genome position nt587 G->A." expected_value: "7" tolerance: null element_identifier: null evidence: intent confidence: medium unresolved: - kind: fixture description: >- No small real Logan-shard kmindex index or Logan-derived LexicMap domain index exists for any of GENOMIC_PHG/GENOMIC_VRL/METAGENOMIC_ENV or Viral/BacteriaMetagenomic; kmindex_db_selection and lexicmap_index_selection therefore cannot be bound to fixtures carrying genuine phiX174 containment content at any tier smaller than usegalaxy.org's production Logan indices, in either test case. blocking: true suggested_resolution: >- Either obtain usegalaxy.org history/API access to run a real (if slow) end-to-end pass, or build a tiny local kmindex/LexicMap index (via kmindex_query's kmindex_build wrapper / lexicmap-index.xml) seeded with cds/E.fasta, cds/J.fasta plus the 3 decoy accessions described in test case gene_e_j_am3_diagnostic_synthetic_lexicmap_index, named to satisfy db_opts|kmindex / db_opts|lexicmap_index's data-table lookup. - kind: fixture description: >- The synthetic 3-decoy LexicMap index (wildtype-clean Gene E, am3-positive Gene E, clean Gene J) that test case gene_e_j_am3_diagnostic_synthetic_lexicmap_index depends on does not yet exist as a buildable artifact; this plan only specifies its required composition and the accession identifiers (E_wildtype_ctrl, E_am3_ctrl, J_clean_ctrl) its assertions reference. blocking: true suggested_resolution: >- implement-galaxy-workflow-test (or a follow-on find-test-data pass) should construct the 3 decoy sequences (derived from real cds/E.fasta / cds/J.fasta with the am3 decoy carrying the exact nt587 G->A substitution) and build/register a tiny LexicMap index from them, or hand-construct the equivalent LexicMap hit-table TSV directly (per test-data-refs.json's confirmed lexicmap_search column schema) if index construction proves impractical. - kind: fixture description: >- Whether kmindex's test-only "register" value and lexicmap's db.lmi+db2.lmi test-data names (used in test case kmindex_wiring_smoke_generic_fixtures) are addressable from a workflow-level Planemo test job the same way they are from each tool's own functional test harness is unconfirmed. blocking: false suggested_resolution: >- Confirm via a trial planemo workflow_test invocation; the plan's existing existence-only assertion design for that test case already tolerates either outcome. - kind: fixture description: >- No verified phiX174-negative-control SRA accession is documented anywhere in the source project (test-data-refs.json gap "no-verified-phix174-negative-control-accession"); a true negative-control test case is therefore out of scope for this plan rather than fabricated. blocking: false suggested_resolution: >- User-supplied: name a specific SRA accession known/expected to have zero phiX174 gene-panel containment, for use as a true-negative case in a future revision of this plan. - kind: output-label description: >- This skill's own declared inputs are the earlier template-era interface/data-flow briefs, but all workflow_label values in this plan were instead taken from the concrete gxformat2 draft (galaxy-workflow.gxwf.yml), per this run's explicit grounding instruction. A strict re-check of every label against the live draft (and against the workflow-label cross-check implement-galaxy-workflow-test already performs) is still worthwhile before finalizing, since this plan itself was not produced by that cross-check tool. blocking: false suggested_resolution: null omissions: - target: "Full production-scale run (10 genes x 109 kmindex shards x up to 25 LexicMap indices, ~2.1M accessions)" reason: >- Explicitly out of scope for a fast workflow test. The real, already-computed full-scale numbers in test-data-refs.json (expected_output_ground_truth_full_scale_only: gene E total_accessions_evaluated=2392457, flagged_internal_stops=2215172, am3_stop_fraction_pct=92.59; gene J total_accessions_evaluated=2278534, flagged_internal_stops=63) are retained only as directional/sanity-bound references for a future full-scale validation pass against usegalaxy.org, not as exact-match assertions in this plan. category: out-of-scope - target: "kmindex_accession_union content assertions, and all lexicmap/streamer/manifest/am3-audit outputs in test case kmindex_wiring_smoke_generic_fixtures" reason: >- No small real Logan-shard kmindex index or Logan-derived LexicMap index exists; content in that test case has no phiX174 biological relationship, so only existence-level checks are asserted there. The content-bearing assertions live in the sibling test case instead. category: no-stable-checkpoint - target: "True negative-control test case (a confirmed phiX174-negative SRA accession)" reason: >- No accession is documented anywhere in the source project as a confirmed phiX174 non-hit; fabricating one would violate the no-fabrication rule this plan inherits from find-test-data (test-data-refs.json gap "no-verified-phix174-negative-control-accession"). category: out-of-scope - target: "LexicMap raw per-gene hit table (lexicmap_search's out_file port)" reason: >- Not a promoted top-level workflow output (absent from galaxy-workflow.gxwf.yml's outputs: block); per galaxy-workflow-testability-design, only labeled workflow-level outputs are assertable by a Galaxy workflow test. This intermediate is exercised only indirectly via lexicmap_streamer_tiling_qc's own outputs. category: no-stable-checkpoint warnings: - code: workflow-label-source-draft-not-brief message: >- This plan's declared inputs are the earlier template-era interface/data-flow briefs, but a concrete gxformat2 workflow draft (galaxy-workflow.gxwf.yml) and resolved test-data-refs.json were additionally available and used for grounding, per this run's explicit instructions. All workflow_label values were taken from the concrete draft's actual input/output ids, not re-derived from the brief's earlier proposed labels, which differ in places (e.g. the brief's prose "Gene E am3 quarantine audit" vs. the draft's actual id gene_e_am3_quarantine_audit). path: "workflow.label_source" - code: missing-fixture message: >- Two shared job inputs (kmindex_db_selection's and lexicmap_index_selection's backing indices) and one entire synthetic fixture (the 3-decoy LexicMap index) have no concrete, buildable location yet; see unresolved[0] and unresolved[1]. path: "test_cases[*].job_inputs" - code: expression-derived-shape message: >- flatten_gene_summary_json_to_row's summary_row TSV column list (used for the ingestion-manifest and per-gene-summary assertions) was taken from galaxy-workflow.gxwf.yml's own step doc text, which itself cites the vendored lexicmap_streamer.py source at a pinned commit; this plan's assertion_intent values are best-effort against that documented contract, not against an actual executed run. path: "test_cases[1].expected_outputs"