Index

_

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

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

A

append_instance() (wfcommons.wfinstances.instance_analyzer.InstanceAnalyzer method) as_dict() (wfcommons.common.file.File method) (wfcommons.common.machine.Machine method) (wfcommons.common.task.Task 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

data_footprint (wfcommons.wfchef.recipes.blast.recipe.BlastRecipe attribute) (wfcommons.wfchef.recipes.bwa.recipe.BwaRecipe attribute) (wfcommons.wfchef.recipes.cycles.recipe.CyclesRecipe attribute) (wfcommons.wfchef.recipes.epigenomics.recipe.EpigenomicsRecipe attribute) (wfcommons.wfchef.recipes.genome.recipe.GenomeRecipe attribute) (wfcommons.wfchef.recipes.montage.recipe.MontageRecipe attribute) (wfcommons.wfchef.recipes.seismology.recipe.SeismologyRecipe attribute) (wfcommons.wfchef.recipes.soykb.recipe.SoykbRecipe attribute) (wfcommons.wfchef.recipes.srasearch.recipe.SrasearchRecipe attribute)

description (wfcommons.wfinstances.logs.makeflow.MakeflowLogsParser attribute) (wfcommons.wfinstances.logs.nextflow.NextflowLogsParser attribute) (wfcommons.wfinstances.logs.pegasus.PegasusLogsParser attribute) draw() (wfcommons.wfinstances.instance.Instance method)

E

EpigenomicsRecipe (class in wfcommons.wfchef.recipes.epigenomics.recipe)

execution_dir (wfcommons.wfinstances.logs.makeflow.MakeflowLogsParser attribute)

F

File (class in wfcommons.common.file)

FileLink (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_rvs() (in module wfcommons.utils) GenomeRecipe (class in wfcommons.wfchef.recipes.genome.recipe)

I

ignore_auxiliary (wfcommons.wfinstances.logs.pegasus.PegasusLogsParser attribute) INPUT (wfcommons.common.file.FileLink attribute) (wfcommons.wfinstances.instance_analyzer.InstanceElement attribute) input_file_size_factor (wfcommons.wfchef.recipes.blast.recipe.BlastRecipe attribute) (wfcommons.wfchef.recipes.bwa.recipe.BwaRecipe attribute) (wfcommons.wfchef.recipes.cycles.recipe.CyclesRecipe attribute) (wfcommons.wfchef.recipes.epigenomics.recipe.EpigenomicsRecipe attribute) (wfcommons.wfchef.recipes.genome.recipe.GenomeRecipe attribute) (wfcommons.wfchef.recipes.montage.recipe.MontageRecipe attribute) (wfcommons.wfchef.recipes.seismology.recipe.SeismologyRecipe attribute) (wfcommons.wfchef.recipes.soykb.recipe.SoykbRecipe attribute) (wfcommons.wfchef.recipes.srasearch.recipe.SrasearchRecipe attribute)

Instance (class in wfcommons.wfinstances.instance) InstanceAnalyzer (class in wfcommons.wfinstances.instance_analyzer) InstanceElement (class in wfcommons.wfinstances.instance_analyzer)

L

leaves() (wfcommons.wfinstances.instance.Instance method) legacy (wfcommons.wfinstances.logs.pegasus.PegasusLogsParser attribute) LINUX (wfcommons.common.machine.MachineSystem attribute) logger (wfcommons.wfchef.recipes.blast.recipe.BlastRecipe attribute) (wfcommons.wfchef.recipes.bwa.recipe.BwaRecipe attribute) (wfcommons.wfchef.recipes.cycles.recipe.CyclesRecipe attribute) (wfcommons.wfchef.recipes.epigenomics.recipe.EpigenomicsRecipe attribute) (wfcommons.wfchef.recipes.genome.recipe.GenomeRecipe attribute) (wfcommons.wfchef.recipes.montage.recipe.MontageRecipe attribute) (wfcommons.wfchef.recipes.seismology.recipe.SeismologyRecipe attribute) (wfcommons.wfchef.recipes.soykb.recipe.SoykbRecipe attribute) (wfcommons.wfchef.recipes.srasearch.recipe.SrasearchRecipe attribute) (wfcommons.wfinstances.logs.makeflow.MakeflowLogsParser attribute) (wfcommons.wfinstances.logs.nextflow.NextflowLogsParser attribute) (wfcommons.wfinstances.logs.pegasus.PegasusLogsParser 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.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) num_tasks (wfcommons.wfchef.recipes.blast.recipe.BlastRecipe attribute) (wfcommons.wfchef.recipes.bwa.recipe.BwaRecipe attribute) (wfcommons.wfchef.recipes.cycles.recipe.CyclesRecipe attribute) (wfcommons.wfchef.recipes.epigenomics.recipe.EpigenomicsRecipe attribute) (wfcommons.wfchef.recipes.genome.recipe.GenomeRecipe attribute) (wfcommons.wfchef.recipes.montage.recipe.MontageRecipe attribute) (wfcommons.wfchef.recipes.seismology.recipe.SeismologyRecipe attribute) (wfcommons.wfchef.recipes.soykb.recipe.SoykbRecipe attribute) (wfcommons.wfchef.recipes.srasearch.recipe.SrasearchRecipe attribute)

O

OUTPUT (wfcommons.common.file.FileLink attribute) (wfcommons.wfinstances.instance_analyzer.InstanceElement attribute) output_file_size_factor (wfcommons.wfchef.recipes.blast.recipe.BlastRecipe attribute) (wfcommons.wfchef.recipes.bwa.recipe.BwaRecipe attribute) (wfcommons.wfchef.recipes.cycles.recipe.CyclesRecipe attribute) (wfcommons.wfchef.recipes.epigenomics.recipe.EpigenomicsRecipe attribute) (wfcommons.wfchef.recipes.genome.recipe.GenomeRecipe attribute) (wfcommons.wfchef.recipes.montage.recipe.MontageRecipe attribute) (wfcommons.wfchef.recipes.seismology.recipe.SeismologyRecipe attribute) (wfcommons.wfchef.recipes.soykb.recipe.SoykbRecipe attribute) (wfcommons.wfchef.recipes.srasearch.recipe.SrasearchRecipe attribute)

P

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

R

read_json() (in module wfcommons.utils) resource_monitor_logs_dir (wfcommons.wfinstances.logs.makeflow.MakeflowLogsParser attribute) roots() (wfcommons.wfinstances.instance.Instance method) RUNTIME (wfcommons.wfinstances.instance_analyzer.InstanceElement attribute) runtime_factor (wfcommons.wfchef.recipes.blast.recipe.BlastRecipe attribute) (wfcommons.wfchef.recipes.bwa.recipe.BwaRecipe attribute) (wfcommons.wfchef.recipes.cycles.recipe.CyclesRecipe attribute) (wfcommons.wfchef.recipes.epigenomics.recipe.EpigenomicsRecipe attribute) (wfcommons.wfchef.recipes.genome.recipe.GenomeRecipe attribute) (wfcommons.wfchef.recipes.montage.recipe.MontageRecipe attribute) (wfcommons.wfchef.recipes.seismology.recipe.SeismologyRecipe attribute) (wfcommons.wfchef.recipes.soykb.recipe.SoykbRecipe attribute) (wfcommons.wfchef.recipes.srasearch.recipe.SrasearchRecipe attribute)

S

SchemaValidator (class in wfcommons.wfinstances.schema) SeismologyRecipe (class in wfcommons.wfchef.recipes.seismology.recipe)

SoykbRecipe (class in wfcommons.wfchef.recipes.soykb.recipe) SrasearchRecipe (class in wfcommons.wfchef.recipes.srasearch.recipe) submit_dir (wfcommons.wfinstances.logs.pegasus.PegasusLogsParser attribute)

T

Task (class in wfcommons.common.task) task_id_counter (wfcommons.wfchef.recipes.blast.recipe.BlastRecipe attribute) (wfcommons.wfchef.recipes.bwa.recipe.BwaRecipe attribute) (wfcommons.wfchef.recipes.cycles.recipe.CyclesRecipe attribute) (wfcommons.wfchef.recipes.epigenomics.recipe.EpigenomicsRecipe attribute) (wfcommons.wfchef.recipes.genome.recipe.GenomeRecipe attribute) (wfcommons.wfchef.recipes.montage.recipe.MontageRecipe attribute) (wfcommons.wfchef.recipes.seismology.recipe.SeismologyRecipe attribute) (wfcommons.wfchef.recipes.soykb.recipe.SoykbRecipe attribute) (wfcommons.wfchef.recipes.srasearch.recipe.SrasearchRecipe attribute) tasks_files (wfcommons.wfchef.recipes.blast.recipe.BlastRecipe attribute) (wfcommons.wfchef.recipes.bwa.recipe.BwaRecipe attribute) (wfcommons.wfchef.recipes.cycles.recipe.CyclesRecipe attribute) (wfcommons.wfchef.recipes.epigenomics.recipe.EpigenomicsRecipe attribute) (wfcommons.wfchef.recipes.genome.recipe.GenomeRecipe attribute) (wfcommons.wfchef.recipes.montage.recipe.MontageRecipe attribute) (wfcommons.wfchef.recipes.seismology.recipe.SeismologyRecipe attribute) (wfcommons.wfchef.recipes.soykb.recipe.SoykbRecipe attribute) (wfcommons.wfchef.recipes.srasearch.recipe.SrasearchRecipe attribute)

tasks_files_names (wfcommons.wfchef.recipes.blast.recipe.BlastRecipe attribute) (wfcommons.wfchef.recipes.bwa.recipe.BwaRecipe attribute) (wfcommons.wfchef.recipes.cycles.recipe.CyclesRecipe attribute) (wfcommons.wfchef.recipes.epigenomics.recipe.EpigenomicsRecipe attribute) (wfcommons.wfchef.recipes.genome.recipe.GenomeRecipe attribute) (wfcommons.wfchef.recipes.montage.recipe.MontageRecipe attribute) (wfcommons.wfchef.recipes.seismology.recipe.SeismologyRecipe attribute) (wfcommons.wfchef.recipes.soykb.recipe.SoykbRecipe attribute) (wfcommons.wfchef.recipes.srasearch.recipe.SrasearchRecipe 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.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) wms_name (wfcommons.wfinstances.logs.makeflow.MakeflowLogsParser attribute) (wfcommons.wfinstances.logs.nextflow.NextflowLogsParser attribute) (wfcommons.wfinstances.logs.pegasus.PegasusLogsParser attribute) wms_url (wfcommons.wfinstances.logs.makeflow.MakeflowLogsParser attribute) (wfcommons.wfinstances.logs.nextflow.NextflowLogsParser attribute) (wfcommons.wfinstances.logs.pegasus.PegasusLogsParser 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)