orthogroups: deep README+AI_GUIDE evaluation pass — bring to phylonam… · 000specific/GIGANTIC@2798129

Validate YAML files: ./gigantic_project-COPYME/subprojects/orthogroups/BLOCK_orthofinder/workflow-COPYME-run_orthofinder/START_HERE-user_config.yaml#L49

49:1 [key-duplicates] duplication of key "cpus" in mapping

Complete job

Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/

Validate YAML files: ./gigantic_project-COPYME/subprojects/trees_gene_groups/gene_groups-COPYME/STEP_3-tree_visualization/workflow-COPYME-tree_visualization/ai/conda_environment.yml#L41

41:5 [indentation] wrong indentation: expected 6 but found 4

Validate YAML files: ./gigantic_project-COPYME/subprojects/trees_gene_groups/gene_groups-snap_family/STEP_3-tree_visualization/workflow-COPYME-tree_visualization/ai/conda_environment.yml#L41

41:5 [indentation] wrong indentation: expected 6 but found 4

Validate YAML files: ./gigantic_project-COPYME/subprojects/orthogroups/BLOCK_orthohmm_GIGANTIC/workflow-COPYME-run_orthohmm_GIGANTIC/ai/conda_environment.yml#L47

47:5 [indentation] wrong indentation: expected 6 but found 4

Validate YAML files: ./gigantic_project-COPYME/subprojects/orthogroups/BLOCK_broccoli/workflow-COPYME-run_broccoli/ai/conda_environment.yml#L52

52:5 [indentation] wrong indentation: expected 6 but found 4

Validate YAML files: ./gigantic_project-COPYME/subprojects/orthogroups/BLOCK_orthohmm/workflow-COPYME-run_orthohmm/ai/conda_environment.yml#L47

47:5 [indentation] wrong indentation: expected 6 but found 4

Validate YAML files: ./gigantic_project-COPYME/subprojects/annotations_hmms/BLOCK_metapredict/workflow-COPYME-run_metapredict/ai/conda_environment.yml#L43

43:5 [indentation] wrong indentation: expected 6 but found 4