Index

A

About add_argument() (pype.utils.arguments.PipelineItemArguments method) add_input() (pype.process.Command method) add_namespace() (pype.process.Command method)

add_output() (pype.process.Command method) add_queue_commands() (pype.utils.queues.SnippetRuntime method) add_queue_id() (pype.utils.queues.SnippetRuntime method) add_volume() (pype.process.Command method) Available modules

B

BatchFileArgument (class in pype.utils.arguments)

BatchListArgument (class in pype.utils.arguments)

C

change_sleep() (pype.utils.queues.SnippetRuntime method) child_close() (pype.process.Command method) close() (pype.process.Command method) Command (class in pype.process)

CommandNamespaceError commit_runtime() (pype.utils.queues.SnippetRuntime method) CompositeArgument (class in pype.utils.arguments) Configuration ConstantArgument (class in pype.utils.arguments)

D

DefaultHelpParser (class in pype.misc)

docker() (pype.process.Command method)

E

EnvModulesError

error() (pype.misc.DefaultHelpParser method)

F

fastq (class in pype.binfmisc)

G

Get started

get_runtime() (pype.utils.queues.SnippetRuntime method)

N

Namespace (class in pype.process)

P

pipe_in() (pype.process.Command method) PipelineError PipelineItemArguments (class in pype.utils.arguments) PipelineItemError Pipelines ProfileError Profiles pype.binfmisc (module)

pype.exceptions (module) pype.logger (module) pype.misc (module) pype.process (module) pype.utils.arguments (module) pype.utils.pipeline (module) pype.utils.profiles (module) pype.utils.queues (module) pype.utils.snippets (module)

Q

queue_depends() (pype.utils.queues.SnippetRuntime method)

R

remove_mode() (pype.process.Volume method) replace_bind_dirname() (pype.process.Volume method)

replace_bind_volume() (pype.process.Volume method) replace_values_in_code() (pype.process.Command method) run() (pype.process.Command method)

S

singularity_volume() (pype.process.Volume method) SnippetError SnippetRuntime (class in pype.utils.queues)

Snippets SubcommandHelpFormatter (class in pype.misc) submit_queue() (pype.utils.queues.SnippetRuntime method)

T

to_dict() (pype.utils.arguments.PipelineItemArguments method)

to_str() (pype.process.Volume method)

V

Volume (class in pype.process)

X

xopen() (in module pype.misc)