Comprehensive Reproducibility Framework for R and Bioinformatics Analysis


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Documentation for package ‘Capsule’ version 0.2.0

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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