Index

_

_load_schema() (wfcommons.wfinstances.schema.SchemaValidator method)

_semantic_validation() (wfcommons.wfinstances.schema.SchemaValidator method) _syntax_validation() (wfcommons.wfinstances.schema.SchemaValidator method)

A

add_dependency() (wfcommons.common.workflow.Workflow method) add_task() (wfcommons.common.workflow.Workflow method) AirflowTranslator (class in wfcommons.wfbench.translator.airflow) append_instance() (wfcommons.wfinstances.instance_analyzer.InstanceAnalyzer method) architecture (wfcommons.common.machine.Machine attribute)

args (wfcommons.common.task.Task attribute) as_dict() (wfcommons.common.file.File method) (wfcommons.common.machine.Machine method) AUXILIARY (wfcommons.common.task.TaskType attribute) avg_cpu (wfcommons.common.task.Task attribute) avg_power (wfcommons.common.task.Task attribute)

B

BashTranslator (class in wfcommons.wfbench.translator.bash) best_fit_distribution() (in module wfcommons.utils) BlastRecipe (class in wfcommons.wfchef.recipes.blast.recipe) build_summary() (wfcommons.wfinstances.instance_analyzer.InstanceAnalyzer method) build_workflow() (wfcommons.wfgen.generator.WorkflowGenerator method) (wfcommons.wfinstances.logs.makeflow.MakeflowLogsParser method) (wfcommons.wfinstances.logs.nextflow.NextflowLogsParser method) (wfcommons.wfinstances.logs.pegasus.PegasusLogsParser method)

build_workflows() (wfcommons.wfgen.generator.WorkflowGenerator method) BwaRecipe (class in wfcommons.wfchef.recipes.bwa.recipe) bytes_read (wfcommons.common.task.Task attribute) bytes_written (wfcommons.common.task.Task attribute)

C

category (wfcommons.common.task.Task attribute) clean_entry() (in module wfcommons.wfbench.bench) cleanup_sys_files() (in module wfcommons.wfbench.bench) COMPUTE (wfcommons.common.task.TaskType attribute) cores (wfcommons.common.task.Task attribute) cpu_cores (wfcommons.common.machine.Machine attribute) cpu_flops (wfcommons.common.machine.Machine attribute)

cpu_speed (wfcommons.common.machine.Machine attribute) cpu_vendor (wfcommons.common.machine.Machine attribute) create_benchmark() (wfcommons.wfbench.bench.WorkflowBenchmark method) create_benchmark_from_input_file() (wfcommons.wfbench.bench.WorkflowBenchmark method) create_benchmark_from_synthetic_workflow() (wfcommons.wfbench.bench.WorkflowBenchmark method) CWLTranslator (class in wfcommons.wfbench.translator.cwl) CyclesRecipe (class in wfcommons.wfchef.recipes.cycles.recipe)

D

DaskTranslator (class in wfcommons.wfbench.translator.dask)

draw() (wfcommons.wfinstances.instance.Instance method)

E

energy (wfcommons.common.task.Task attribute)

EpigenomicsRecipe (class in wfcommons.wfchef.recipes.epigenomics.recipe) execution_as_dict() (wfcommons.common.task.Task method)

F

File (class in wfcommons.common.file)

G

generate_all_fit_plots() (wfcommons.wfinstances.instance_analyzer.InstanceAnalyzer method) generate_fit_plots() (wfcommons.wfinstances.instance_analyzer.InstanceAnalyzer method) generate_input_file() (wfcommons.wfbench.bench.WorkflowBenchmark method) generate_json() (wfcommons.common.workflow.Workflow method)

generate_rvs() (in module wfcommons.utils) generate_stderr_files (wfcommons.wfbench.translator.cwl.CWLTranslator attribute) generate_stdout_files (wfcommons.wfbench.translator.cwl.CWLTranslator attribute) generate_sys_data() (in module wfcommons.wfbench.bench) GenomeRecipe (class in wfcommons.wfchef.recipes.genome.recipe)

I

ignore_auxiliary (wfcommons.wfinstances.logs.pegasus.PegasusLogsParser attribute) INPUT (wfcommons.wfinstances.instance_analyzer.InstanceElement attribute) input_files (wfcommons.common.task.Task attribute) Instance (class in wfcommons.wfinstances.instance)

InstanceAnalyzer (class in wfcommons.wfinstances.instance_analyzer) InstanceElement (class in wfcommons.wfinstances.instance_analyzer) instances (wfcommons.wfinstances.instance_analyzer.InstanceAnalyzer attribute) instances_summary (wfcommons.wfinstances.instance_analyzer.InstanceAnalyzer attribute)

L

launch_dir (wfcommons.common.task.Task attribute) leaves() (wfcommons.common.workflow.Workflow method) (wfcommons.wfinstances.instance.Instance method)

LINUX (wfcommons.common.machine.MachineSystem attribute) logger (wfcommons.common.machine.Machine attribute) (wfcommons.common.task.Task attribute) (wfcommons.wfinstances.instance_analyzer.InstanceAnalyzer attribute)

M

Machine (class in wfcommons.common.machine) machines (wfcommons.common.task.Task attribute) MachineSystem (class in wfcommons.common.machine) MACOS (wfcommons.common.machine.MachineSystem attribute) MakeflowLogsParser (class in wfcommons.wfinstances.logs.makeflow) MakeflowTranslator (class in wfcommons.wfbench.translator.makeflow) memory (wfcommons.common.machine.Machine attribute) (wfcommons.common.task.Task attribute) mf_file (wfcommons.wfinstances.logs.makeflow.MakeflowLogsParser attribute) mf_log_file (wfcommons.wfinstances.logs.makeflow.MakeflowLogsParser attribute) module wfcommons.common.file wfcommons.common.machine wfcommons.common.task wfcommons.common.workflow wfcommons.utils wfcommons.wfbench.bench wfcommons.wfbench.translator.airflow wfcommons.wfbench.translator.bash wfcommons.wfbench.translator.cwl wfcommons.wfbench.translator.dask wfcommons.wfbench.translator.makeflow wfcommons.wfbench.translator.nextflow wfcommons.wfbench.translator.parsl wfcommons.wfbench.translator.pegasus wfcommons.wfbench.translator.pycompss wfcommons.wfbench.translator.streamflow wfcommons.wfbench.translator.swift_t wfcommons.wfbench.translator.taskvine wfcommons.wfchef.recipes.blast.recipe wfcommons.wfchef.recipes.bwa.recipe wfcommons.wfchef.recipes.cycles.recipe wfcommons.wfchef.recipes.epigenomics.recipe wfcommons.wfchef.recipes.genome.recipe wfcommons.wfchef.recipes.montage.recipe wfcommons.wfchef.recipes.rnaseq.recipe wfcommons.wfchef.recipes.seismology.recipe wfcommons.wfchef.recipes.soykb.recipe wfcommons.wfchef.recipes.srasearch.recipe wfcommons.wfgen.generator wfcommons.wfinstances.instance wfcommons.wfinstances.instance_analyzer wfcommons.wfinstances.logs.makeflow wfcommons.wfinstances.logs.nextflow wfcommons.wfinstances.logs.pegasus wfcommons.wfinstances.schema

MontageRecipe (class in wfcommons.wfchef.recipes.montage.recipe)

N

name (wfcommons.common.machine.Machine attribute) (wfcommons.common.task.Task attribute) ncr() (in module wfcommons.utils)

NextflowLogsParser (class in wfcommons.wfinstances.logs.nextflow) NextflowTranslator (class in wfcommons.wfbench.translator.nextflow) NoValue (class in wfcommons.utils)

O

OUTPUT (wfcommons.wfinstances.instance_analyzer.InstanceElement attribute)

output_files (wfcommons.common.task.Task attribute)

P

ParslTranslator (class in wfcommons.wfbench.translator.parsl) PegasusLogsParser (class in wfcommons.wfinstances.logs.pegasus) PegasusTranslator (class in wfcommons.wfbench.translator.pegasus)

priority (wfcommons.common.task.Task attribute) program (wfcommons.common.task.Task attribute) PyCompssTranslator (class in wfcommons.wfbench.translator.pycompss)

R

read_dot() (wfcommons.common.workflow.Workflow method) read_json() (in module wfcommons.utils) release (wfcommons.common.machine.Machine attribute) RnaseqRecipe (class in wfcommons.wfchef.recipes.rnaseq.recipe)

roots() (wfcommons.common.workflow.Workflow method) (wfcommons.wfinstances.instance.Instance method) runtime (wfcommons.common.task.Task attribute) RUNTIME (wfcommons.wfinstances.instance_analyzer.InstanceElement attribute)

S

SchemaValidator (class in wfcommons.wfinstances.schema) SeismologyRecipe (class in wfcommons.wfchef.recipes.seismology.recipe) SoykbRecipe (class in wfcommons.wfchef.recipes.soykb.recipe) specification_as_dict() (wfcommons.common.task.Task method) SrasearchRecipe (class in wfcommons.wfchef.recipes.srasearch.recipe) start_time (wfcommons.common.task.Task attribute)

StreamflowTranslator (class in wfcommons.wfbench.translator.streamflow) submit_dir (wfcommons.wfinstances.logs.pegasus.PegasusLogsParser attribute) SUBWORKFLOW (wfcommons.common.task.TaskType attribute) subworkflows (wfcommons.wfbench.translator.nextflow.NextflowTranslator attribute) SwiftTTranslator (class in wfcommons.wfbench.translator.swift_t) system (wfcommons.common.machine.Machine attribute)

T

Task (class in wfcommons.common.task) task_id (wfcommons.common.task.Task attribute) tasks_summary (wfcommons.wfinstances.instance_analyzer.InstanceAnalyzer attribute) TaskType (class in wfcommons.common.task) TaskVineTranslator (class in wfcommons.wfbench.translator.taskvine) to_nx_digraph() (wfcommons.common.workflow.Workflow method) TRANSFER (wfcommons.common.task.TaskType attribute) translate() (wfcommons.wfbench.translator.airflow.AirflowTranslator method) (wfcommons.wfbench.translator.bash.BashTranslator method) (wfcommons.wfbench.translator.cwl.CWLTranslator method) (wfcommons.wfbench.translator.dask.DaskTranslator method) (wfcommons.wfbench.translator.makeflow.MakeflowTranslator method) (wfcommons.wfbench.translator.nextflow.NextflowTranslator method) (wfcommons.wfbench.translator.parsl.ParslTranslator method) (wfcommons.wfbench.translator.pegasus.PegasusTranslator method) (wfcommons.wfbench.translator.pycompss.PyCompssTranslator method) (wfcommons.wfbench.translator.streamflow.StreamflowTranslator method) (wfcommons.wfbench.translator.swift_t.SwiftTTranslator method) (wfcommons.wfbench.translator.taskvine.TaskVineTranslator method)

type (wfcommons.common.task.Task attribute)

V

validate_instance() (wfcommons.wfinstances.schema.SchemaValidator method)

W

wfcommons.common.file module wfcommons.common.machine module wfcommons.common.task module wfcommons.common.workflow module wfcommons.utils module wfcommons.wfbench.bench module wfcommons.wfbench.translator.airflow module wfcommons.wfbench.translator.bash module wfcommons.wfbench.translator.cwl module wfcommons.wfbench.translator.dask module wfcommons.wfbench.translator.makeflow module wfcommons.wfbench.translator.nextflow module wfcommons.wfbench.translator.parsl module wfcommons.wfbench.translator.pegasus module wfcommons.wfbench.translator.pycompss module wfcommons.wfbench.translator.streamflow module wfcommons.wfbench.translator.swift_t module wfcommons.wfbench.translator.taskvine module wfcommons.wfchef.recipes.blast.recipe module

wfcommons.wfchef.recipes.bwa.recipe module wfcommons.wfchef.recipes.cycles.recipe module wfcommons.wfchef.recipes.epigenomics.recipe module wfcommons.wfchef.recipes.genome.recipe module wfcommons.wfchef.recipes.montage.recipe module wfcommons.wfchef.recipes.rnaseq.recipe module wfcommons.wfchef.recipes.seismology.recipe module wfcommons.wfchef.recipes.soykb.recipe module wfcommons.wfchef.recipes.srasearch.recipe module wfcommons.wfgen.generator module wfcommons.wfinstances.instance module wfcommons.wfinstances.instance_analyzer module wfcommons.wfinstances.logs.makeflow module wfcommons.wfinstances.logs.nextflow module wfcommons.wfinstances.logs.pegasus module wfcommons.wfinstances.schema module WINDOWS (wfcommons.common.machine.MachineSystem attribute) Workflow (class in wfcommons.common.workflow) WorkflowBenchmark (class in wfcommons.wfbench.bench) WorkflowGenerator (class in wfcommons.wfgen.generator) write_dot() (wfcommons.common.workflow.Workflow method) (wfcommons.wfinstances.instance.Instance method) write_json() (wfcommons.common.workflow.Workflow method)