Table of Contents - bio-pipengine-0.9.7 Documentation
Pages
- LICENSE
-
README
- PipEngine
- Installation
- :: Topics ::
- :: Usage ::
- Command line for RUN mode
- :: The Pipeline YAML ::
- Resources definition
- Step definition
- :: The Samples YAML ::
- Sample groups
- How to create the Samples file
- :: Input and output conventions ::
- How steps are connected together
- Jobs dependencies
- :: Multi-Samples and complex steps ::
- Composable & Modular steps definition
- Dry Run
- Temporary output folder
- One job with multiple steps
- :: Examples ::
- Example 1: One step and multiple command lines
- Example 2: Multiple steps in one job
- Logging
- :: PBS Options ::
- :: Extending and contributing ::
- Copyright
Classes and Modules
Methods
- ::add_job — Bio::Pipengine
- ::check_and_run_multi — Bio::Pipengine
- ::check_samples — Bio::Pipengine
- ::check_steps — Bio::Pipengine
- ::create_job — Bio::Pipengine
- ::create_samples — Bio::Pipengine
- ::include — Bio::Pipengine
- ::inspect_steps — Bio::Pipengine
- ::load_samples_file — Bio::Pipengine
- ::new — Bio::Pipengine::Job
- ::new — Bio::Pipengine::Sample
- ::new — Bio::Pipengine::Step
- ::parse_tag_option — Bio::Pipengine
- ::run — Bio::Pipengine
- #add_resources — Bio::Pipengine::Job
- #add_step — Bio::Pipengine::Job
- #generate_cmd_line — Bio::Pipengine::Job
- #generate_multi_cmd — Bio::Pipengine::Job
- #generate_uuid — Bio::Pipengine::Job
- #group — Bio::Pipengine::Sample
- #group= — Bio::Pipengine::Sample
- #has_prerequisite? — Bio::Pipengine::Step
- #is_multi? — Bio::Pipengine::Step
- #logger — Bio::Pipengine::Job
- #name — Bio::Pipengine::Sample
- #name= — Bio::Pipengine::Sample
- #output — Bio::Pipengine::Job
- #parse_yaml — Bio::Pipengine::Step
- #set_multi_cmd — Bio::Pipengine::Job
- #split_and_sub — Bio::Pipengine::Job
- #sub_multi — Bio::Pipengine::Job
- #sub_placeholders — Bio::Pipengine::Job
- #sub_resources_and_cpu — Bio::Pipengine::Job
- #submit — Bio::Pipengine::Job
- #to_script — Bio::Pipengine::Job
- #x_name — Bio::Pipengine::Sample