WfCommons
v0.8
Quickstart
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User Guide
The WfCommons Project
Parsing Workflow Execution Logs
Analyzing Instances
Generating Workflows Recipes
Generating Workflows
API Reference
User API Reference
Developer API Reference
WfCommons
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Index
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Index
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A
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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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I
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L
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M
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N
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O
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P
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R
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S
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T
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V
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W
_
_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)
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