WfCommons
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The WfCommons Project
WfInstances: Workflow Instances
WfChef: Workflows Recipes
WfGen: Generating Workflows
WfBench: Workflow Benchmarks
API Reference
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Developer API Reference
WfCommons
Index
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Index
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B
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C
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D
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E
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F
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G
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H
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M
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W
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_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)
(wfcommons.common.task.Task method)
assigning_correct_files() (in module wfcommons.wfbench.bench)
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
cleanup_sys_files() (in module wfcommons.wfbench.bench)
COMPUTE (wfcommons.common.task.TaskType 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)
CyclesRecipe (class in wfcommons.wfchef.recipes.cycles.recipe)
D
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_input_file() (wfcommons.wfbench.bench.WorkflowBenchmark method)
generate_rvs() (in module wfcommons.utils)
generate_sys_data() (in module wfcommons.wfbench.bench)
GenomeRecipe (class in wfcommons.wfchef.recipes.genome.recipe)
H
human_readable_memory() (in module wfcommons.wfbench.translator.nextflow)
I
ignore_auxiliary (wfcommons.wfinstances.logs.pegasus.PegasusLogsParser attribute)
INPUT (wfcommons.common.file.FileLink attribute)
(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)
L
leaves() (wfcommons.common.workflow.Workflow method)
(wfcommons.wfinstances.instance.Instance method)
LINUX (wfcommons.common.machine.MachineSystem attribute)
logger (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.wfbench.bench
wfcommons.wfbench.translator.nextflow
wfcommons.wfbench.translator.pegasus
wfcommons.wfbench.translator.swift_t
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)
NextflowTranslator (class in wfcommons.wfbench.translator.nextflow)
NoValue (class in wfcommons.utils)
O
OUTPUT (wfcommons.common.file.FileLink attribute)
(wfcommons.wfinstances.instance_analyzer.InstanceElement attribute)
P
PegasusLogsParser (class in wfcommons.wfinstances.logs.pegasus)
PegasusTranslator (class in wfcommons.wfbench.translator.pegasus)
R
read_dot() (wfcommons.common.workflow.Workflow method)
read_json() (in module wfcommons.utils)
resource_monitor_logs_dir (wfcommons.wfinstances.logs.makeflow.MakeflowLogsParser attribute)
roots() (wfcommons.common.workflow.Workflow method)
(wfcommons.wfinstances.instance.Instance method)
run() (wfcommons.wfbench.bench.WorkflowBenchmark 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)
SrasearchRecipe (class in wfcommons.wfchef.recipes.srasearch.recipe)
submit_dir (wfcommons.wfinstances.logs.pegasus.PegasusLogsParser attribute)
SUBWORKFLOW (wfcommons.common.task.TaskType attribute)
SwiftTTranslator (class in wfcommons.wfbench.translator.swift_t)
T
Task (class in wfcommons.common.task)
TaskType (class in wfcommons.common.task)
to_nx_digraph() (wfcommons.common.workflow.Workflow method)
TRANSFER (wfcommons.common.task.TaskType attribute)
translate() (wfcommons.wfbench.translator.nextflow.NextflowTranslator method)
(wfcommons.wfbench.translator.pegasus.PegasusTranslator method)
(wfcommons.wfbench.translator.swift_t.SwiftTTranslator method)
V
valid_task_name() (wfcommons.wfbench.translator.nextflow.NextflowTranslator method)
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.nextflow
module
wfcommons.wfbench.translator.pegasus
module
wfcommons.wfbench.translator.swift_t
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)
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)
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