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) append_instance() (wfcommons.wfinstances.instance_analyzer.InstanceAnalyzer method)

as_dict() (wfcommons.common.file.File method) (wfcommons.common.machine.Machine method) AUXILIARY (wfcommons.common.task.TaskType attribute)

B

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)

C

COMPUTE (wfcommons.common.task.TaskType attribute)

CyclesRecipe (class in wfcommons.wfchef.recipes.cycles.recipe)

D

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

E

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_json() (wfcommons.common.workflow.Workflow method) generate_rvs() (in module wfcommons.utils) GenomeRecipe (class in wfcommons.wfchef.recipes.genome.recipe)

I

ignore_auxiliary (wfcommons.wfinstances.logs.pegasus.PegasusLogsParser attribute) INPUT (wfcommons.wfinstances.instance_analyzer.InstanceElement 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

leaves() (wfcommons.common.workflow.Workflow method) (wfcommons.wfinstances.instance.Instance method)

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

M

Machine (class in wfcommons.common.machine) MachineSystem (class in wfcommons.common.machine) MACOS (wfcommons.common.machine.MachineSystem attribute) MakeflowLogsParser (class in wfcommons.wfinstances.logs.makeflow) 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.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

ncr() (in module wfcommons.utils)

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

O

OUTPUT (wfcommons.wfinstances.instance_analyzer.InstanceElement attribute)

P

PegasusLogsParser (class in wfcommons.wfinstances.logs.pegasus)

R

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

roots() (wfcommons.common.workflow.Workflow method) (wfcommons.wfinstances.instance.Instance method) 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) submit_dir (wfcommons.wfinstances.logs.pegasus.PegasusLogsParser attribute) SUBWORKFLOW (wfcommons.common.task.TaskType attribute)

T

Task (class in wfcommons.common.task) tasks_summary (wfcommons.wfinstances.instance_analyzer.InstanceAnalyzer attribute)

TaskType (class in wfcommons.common.task) to_nx_digraph() (wfcommons.common.workflow.Workflow method) TRANSFER (wfcommons.common.task.TaskType 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.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) 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)