Skip to content

Commit dcc5358

Browse files
000specificclaude
000specific
and
claude
committed
annotations_X_ocl: update upload_manifest for the 4-type framework
Drop the dead per-subtype 1-output entries (annogroups-single/combo/zero + subtypes_manifest -- no longer produced) and rename the per-type OCL summaries to feature/combination/architecture (absent is excluded from OCL). Set the curated publish set. RUN_03 published to the server (supersedes RUN_02). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
1 parent b7e6288 commit dcc5358

1 file changed

Lines changed: 24 additions & 21 deletions

File tree

  • gigantic_project-COPYME/subprojects/ocl_phylogenetic_structures/BLOCK_annotations_X_ocl/workflow-COPYME-ocl_analysis

‎gigantic_project-COPYME/subprojects/ocl_phylogenetic_structures/BLOCK_annotations_X_ocl/workflow-COPYME-ocl_analysis/upload_manifest.tsv‎

Lines changed: 24 additions & 21 deletions
Original file line numberDiff line numberDiff line change
@@ -9,6 +9,13 @@
99
# Destination (auto-derived by shared helper):
1010
# upload_to_server/BLOCK_annotations_X_ocl/workflow-RUN_N/structure_NNN/N-output/
1111
#
12+
# Annogroups are IMPORTED from the annogroups subproject (four-type framework:
13+
# feature, combination, architecture, absent). OCL maps the origin-bearing types
14+
# (absent excluded) onto each structure, so the per-type OCL summaries are
15+
# feature / combination / architecture. Script 001 emits annogroup_map +
16+
# annogroups-species_identifiers only (no per-type 1-output tables, no subtypes
17+
# manifest -- those were the old single/combo/zero scheme).
18+
#
1219
# Policy: each subproject hosts its OWN outputs only. The phylogenetic
1320
# substrate files (parent_child_table, phylogenetic_blocks, phylogenetic_paths,
1421
# clade_mappings) are INPUTS copied from trees_species; they are hosted under
@@ -18,31 +25,27 @@
1825
source_path include dest_name display_label file_category description order dir_label
1926
#
2027
# ----- Annogroup input maps (per-structure, published as scientific context) -----
21-
OUTPUT_pipeline/structure_*/1-output/1_ai-structure_*_annogroup_map.tsv no Annogroup map data Annogroup ID → annotation identifier mapping. 10 annogroup tables
22-
OUTPUT_pipeline/structure_*/1-output/1_ai-structure_*_annogroup_subtypes_manifest.tsv no Annogroup subtypes manifest data Classification of annogroups into combo/single/zero subtypes. 12 annogroup tables
23-
OUTPUT_pipeline/structure_*/1-output/1_ai-structure_*_annogroups-combo.tsv no Annogroups — combo data Combo-subtype annogroup table. 14 annogroup tables
24-
OUTPUT_pipeline/structure_*/1-output/1_ai-structure_*_annogroups-single.tsv no Annogroups — single data Single-subtype annogroup table. 16 annogroup tables
25-
OUTPUT_pipeline/structure_*/1-output/1_ai-structure_*_annogroups-zero.tsv no Annogroups — zero data Zero-subtype annogroup table. 18 annogroup tables
26-
OUTPUT_pipeline/structure_*/1-output/1_ai-structure_*_annogroups-species_identifiers.tsv no Annogroups — species identifiers data Species-identifier mapping within each annogroup. 19 annogroup tables
28+
OUTPUT_pipeline/structure_*/1-output/1_ai-structure_*_annogroup_map.tsv yes Annogroup map data Annogroup ID to annotation accessions/definitions mapping (imported from the annogroups subproject). 10 annogroup tables
29+
OUTPUT_pipeline/structure_*/1-output/1_ai-structure_*_annogroups-species_identifiers.tsv yes Annogroups — species identifiers data Per-annogroup type, species list, accessions and definitions (the OCL-standardized annogroup table). 19 annogroup tables
2730
#
2831
# ----- Tier 3 -- interpretable OCL results (per structure, all 105) -----
29-
OUTPUT_pipeline/structure_*/4-output/4_ai-structure_*_annogroups-complete_ocl_summary-all_types.tsv no Annogroups OCL summary — all types summary Full OCL summary across all annogroup subtypes. 30 OCL summaries
30-
OUTPUT_pipeline/structure_*/4-output/4_ai-structure_*_annogroups-complete_ocl_summary-combo.tsv no Annogroups OCL summary — combo summary OCL summary restricted to combo-subtype annogroups. 32 OCL summaries
31-
OUTPUT_pipeline/structure_*/4-output/4_ai-structure_*_annogroups-complete_ocl_summary-single.tsv no Annogroups OCL summary — single summary OCL summary restricted to single-subtype annogroups. 34 OCL summaries
32-
OUTPUT_pipeline/structure_*/4-output/4_ai-structure_*_annogroups-complete_ocl_summary-zero.tsv no Annogroups OCL summary — zero summary OCL summary restricted to zero-subtype annogroups. 36 OCL summaries
33-
OUTPUT_pipeline/structure_*/4-output/4_ai-structure_*_path_states-per_annogroup_per_species.tsv no Path states (annogroup × species) data Path-state matrix per annogroup per species — the novel biological deliverable. 40 OCL summaries
34-
OUTPUT_pipeline/structure_*/4-output/4_ai-structure_*_clades-comprehensive_statistics.tsv no Clades — comprehensive statistics data Per-clade annogroup/conservation/loss statistics. 42 OCL summaries
35-
OUTPUT_pipeline/structure_*/4-output/4_ai-structure_*_species-summaries.tsv no Species summaries data Per-species annogroup-presence summary. 44 OCL summaries
36-
OUTPUT_pipeline/structure_*/3-output/3_ai-structure_*_conservation_loss-per_block.tsv no Conservation/loss per phylogenetic block data Conservation and loss events per parent::child edge. 50 conservation and loss
37-
OUTPUT_pipeline/structure_*/3-output/3_ai-structure_*_conservation_loss-summary.tsv no Conservation/loss summary summary Aggregated conservation/loss metrics. 52 conservation and loss
38-
OUTPUT_pipeline/structure_*/2-output/2_ai-structure_*_annogroup_origins.tsv no Annogroup origins data Inferred origin clade for each annogroup. 60 annogroup origins
39-
OUTPUT_pipeline/structure_*/2-output/2_ai-structure_*_origins_summary-annogroups_per_clade.tsv no Origins summary (annogroups per clade) summary Count of annogroups originating at each clade. 62 annogroup origins
40-
OUTPUT_pipeline/structure_*/4-output/4_ai-structure_*_validation_report.txt no Validation report qc Integrity checks for the OCL analysis. 70 OCL summaries
41-
OUTPUT_pipeline/structure_*/5-output/5_ai-structure_*_qc_metrics.tsv no QC metrics qc Final QC metrics for this structure's OCL analysis. 72 QC metrics
32+
OUTPUT_pipeline/structure_*/4-output/4_ai-structure_*_annogroups-complete_ocl_summary-all_types.tsv yes Annogroups OCL summary — all types summary Full OCL summary across all annogroup types (feature, combination, architecture). 30 OCL summaries
33+
OUTPUT_pipeline/structure_*/4-output/4_ai-structure_*_annogroups-complete_ocl_summary-feature.tsv yes Annogroups OCL summary — feature summary OCL summary restricted to feature annogroups (one shared feature each). 32 OCL summaries
34+
OUTPUT_pipeline/structure_*/4-output/4_ai-structure_*_annogroups-complete_ocl_summary-combination.tsv yes Annogroups OCL summary — combination summary OCL summary restricted to combination annogroups (shared distinct feature set). 34 OCL summaries
35+
OUTPUT_pipeline/structure_*/4-output/4_ai-structure_*_annogroups-complete_ocl_summary-architecture.tsv yes Annogroups OCL summary — architecture summary OCL summary restricted to architecture annogroups (shared ordered feature arrangement). 36 OCL summaries
36+
OUTPUT_pipeline/structure_*/4-output/4_ai-structure_*_path_states-per_annogroup_per_species.tsv yes Path states (annogroup × species) data Path-state matrix per annogroup per species — the novel biological deliverable. 40 OCL summaries
37+
OUTPUT_pipeline/structure_*/4-output/4_ai-structure_*_clades-comprehensive_statistics.tsv yes Clades — comprehensive statistics data Per-clade annogroup/conservation/loss statistics. 42 OCL summaries
38+
OUTPUT_pipeline/structure_*/4-output/4_ai-structure_*_species-summaries.tsv yes Species summaries data Per-species annogroup-presence summary. 44 OCL summaries
39+
OUTPUT_pipeline/structure_*/3-output/3_ai-structure_*_conservation_loss-per_block.tsv yes Conservation/loss per phylogenetic block data Conservation and loss events per parent::child edge. 50 conservation and loss
40+
OUTPUT_pipeline/structure_*/3-output/3_ai-structure_*_conservation_loss-summary.tsv yes Conservation/loss summary summary Aggregated conservation/loss metrics. 52 conservation and loss
41+
OUTPUT_pipeline/structure_*/2-output/2_ai-structure_*_annogroup_origins.tsv yes Annogroup origins data Inferred origin clade for each annogroup. 60 annogroup origins
42+
OUTPUT_pipeline/structure_*/2-output/2_ai-structure_*_origins_summary-annogroups_per_clade.tsv yes Origins summary (annogroups per clade) summary Count of annogroups originating at each clade. 62 annogroup origins
43+
OUTPUT_pipeline/structure_*/4-output/4_ai-structure_*_validation_report.txt yes Validation report qc Integrity checks for the OCL analysis. 70 OCL summaries
44+
OUTPUT_pipeline/structure_*/5-output/5_ai-structure_*_qc_metrics.tsv yes QC metrics qc Final QC metrics for this structure's OCL analysis. 72 QC metrics
4245
#
4346
# ----- Tier 4 -- raw / massive per-structure reference tables -----
44-
OUTPUT_pipeline/structure_*/3-output/3_ai-structure_*_conservation_patterns-per_annogroup.tsv no Conservation patterns per annogroup data Full per-annogroup conservation-pattern table. 80 conservation and loss
45-
OUTPUT_pipeline/structure_*/2-output/*_annogroups_by_origin/*.txt no Annogroups by origin (per-clade lists) data Per-origin annogroup ID lists — one .txt per origin clade. 84 annogroup origins
47+
OUTPUT_pipeline/structure_*/3-output/3_ai-structure_*_conservation_patterns-per_annogroup.tsv yes Conservation patterns per annogroup data Full per-annogroup conservation-pattern table. 80 conservation and loss
48+
OUTPUT_pipeline/structure_*/2-output/*_annogroups_by_origin/*.txt yes Annogroups by origin (per-clade lists) data Per-origin annogroup ID lists — one .txt per origin clade. 84 annogroup origins
4649
#
4750
# ----- Phylogenetic substrate (species-tree inputs) — NOT hosted here -----
4851
# Policy: each subproject hosts only its OWN outputs. These are inputs copied

0 commit comments

Comments
 (0)