Man pages for Capsule
Comprehensive Reproducibility Framework for R and Bioinformatics Analysis
| capture_environment | Capture Environment State |
| capture_hardware | Capture Hardware Information |
| capture_session | Capture Complete Session Information |
| capture_system_libraries | Capture System Libraries |
| compare_snapshots | Compare Two Workflow Snapshots |
| create_renv_lockfile | Create renv Lockfile |
| create_repro_report | Create Reproducibility Report |
| dot-build_dependency_graph | Build Dependency Graph |
| dot-calculate_checksum | Calculate Checksum with Smart Algorithm Selection |
| dot-compare_packages | Compare Package Lists |
| dot-compare_registries | Compare Registry Files |
| dot-create_config | Create Capsule config |
| dot-create_example_script | Create example workflow script |
| dot-create_gitignore | Create .gitignore |
| dot-extract_package_info | Extract Package Information |
| dot-format_r_value | Format R Value for Script |
| dot-format_size | Format File Size |
| dot-generate_comparison_report | Generate Comparison Report |
| dot-generate_docker_compose | Generate docker-compose.yml |
| dot-generate_dockerfile | Generate Dockerfile |
| dot-generate_dockerignore | Generate .dockerignore |
| dot-generate_docker_readme | Generate Docker README |
| dot-get_fasta_stats | Get FASTA Statistics |
| dot-get_tool_path | Get Tool Path |
| dot-get_tool_version | Get Tool Version String |
| dot-load_conda_registry | Load Conda Registry |
| dot-load_param_registry | Load Parameter Registry |
| dot-load_reference_registry | Load Reference Registry |
| dot-load_registry | Load Provenance Registry |
| dot-load_seed_registry | Load Seed Registry |
| dot-load_tools_registry | Load Tools Registry |
| dot-parse_deps | Parse Package Dependencies |
| dot-save_conda_registry | Save Conda Registry |
| dot-save_param_registry | Save Parameter Registry |
| dot-save_reference_registry | Save Reference Registry |
| dot-save_registry | Save Provenance Registry |
| dot-save_seed_registry | Save Seed Registry |
| dot-save_tools_registry | Save Tools Registry |
| export_for_cwl | Generate CWL (Common Workflow Language) Input |
| export_for_nextflow | Export Capsule Data for Nextflow |
| export_for_snakemake | Export Capsule Data for Snakemake |
| export_for_wdl | Create WDL (Workflow Description Language) Config |
| generate_docker | Generate Docker Configuration |
| generate_repro_script | Generate Reproducible Script |
| generate_singularity | Generate Singularity Definition File |
| get_conda_env_info | Get Conda Environment Info |
| get_data_lineage | Get Data Lineage |
| get_param_history | Get Parameter History |
| get_reference_info | Get Reference Genome Information |
| get_seed_history | Get Seed History |
| get_tool_versions | Get External Tool Versions |
| init_capsule | Initialize Capsule in Project |
| list_reference_sources | List Common Reference Genome Sources |
| list_snapshots | List Available Snapshots |
| restore_conda_env | Restore Conda Environment |
| restore_seed | Restore Random Seed |
| set_seed | Set and Track Random Seed |
| snapshot_packages | Track Package Versions and Dependencies |
| snapshot_workflow | Create Complete Workflow Snapshot |
| track_conda_env | Track Conda Environment |
| track_data | Track Data Provenance |
| track_external_tools | Track External Bioinformatics Tools |
| track_params | Track Analysis Parameters |
| track_reference_genome | Track Reference Genome |
| verify_data | Verify Data Integrity |
