Comprehensive Reproducibility Framework for R and Bioinformatics
Analysis
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Documentation for package ‘Capsule’ version 0.2.0
Help Pages
| 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 |
| 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 |