Index

A

all_outputs_exist() (in module step_pipeline.utils) always_run() (step_pipeline.batch.BatchStep method)

are_any_inputs_missing() (in module step_pipeline.utils) are_output_files_up_to_date() (in module step_pipeline.utils) are_outputs_up_to_date() (in module step_pipeline.utils)

B

Backend (class in step_pipeline.constants) backend (step_pipeline.batch.BatchPipeline property) (step_pipeline.wdl.WdlPipeline property) BASH (step_pipeline.batch.BatchStepType attribute)

BatchPipeline (class in step_pipeline.batch) BatchStep (class in step_pipeline.batch) BatchStepType (class in step_pipeline.batch) BOOL (step_pipeline.io.InputType attribute)

C

cancel() (step_pipeline.pipeline.Step method) cancel_after_n_failures() (step_pipeline.batch.BatchPipeline method) (step_pipeline.pipeline.Pipeline method) check_gcloud_storage_region() (in module step_pipeline.utils) check_input_glob() (step_pipeline.pipeline.Pipeline method) command() (step_pipeline.pipeline.Step method)

COPY (step_pipeline.io.Delocalize attribute) (step_pipeline.io.Localize attribute) cpu() (step_pipeline.batch.BatchStep method) (step_pipeline.wdl.WdlStep method) CROMWELL (step_pipeline.constants.Backend attribute), [1] custom_machine_type() (step_pipeline.batch.BatchStep method)

D

default_cpu() (step_pipeline.batch.BatchPipeline method) (step_pipeline.pipeline.Pipeline method) default_custom_machine_type() (step_pipeline.batch.BatchPipeline method) default_image() (step_pipeline.batch.BatchPipeline method) (step_pipeline.pipeline.Pipeline method) default_memory() (step_pipeline.batch.BatchPipeline method) (step_pipeline.pipeline.Pipeline method) default_output_dir() (step_pipeline.pipeline.Pipeline method) default_preemptible() (step_pipeline.batch.BatchPipeline method)

default_python_image() (step_pipeline.batch.BatchPipeline method) (step_pipeline.pipeline.Pipeline method) default_storage() (step_pipeline.batch.BatchPipeline method) (step_pipeline.pipeline.Pipeline method) default_timeout() (step_pipeline.batch.BatchPipeline method) (step_pipeline.pipeline.Pipeline method) Delocalize (class in step_pipeline.io) delocalize_by (step_pipeline.io.OutputSpec property) depends_on() (step_pipeline.pipeline.Step method) download_to_dir (step_pipeline.io.OutputSpec property)

E

export_pipeline_graph() (step_pipeline.pipeline.Pipeline method)

F

filename (step_pipeline.io.InputSpec property) (step_pipeline.io.OutputSpec property)

files_exist() (in module step_pipeline.utils) FLOAT (step_pipeline.io.InputType attribute)

G

gcloud_auth_activate_service_account() (step_pipeline.pipeline.Step method) gcloud_project() (step_pipeline.batch.BatchPipeline method) (step_pipeline.pipeline.Pipeline method) get_config_arg_parser() (step_pipeline.pipeline.Pipeline method) get_config_arg_parser_group() (step_pipeline.pipeline.Pipeline method) get_inputs() (step_pipeline.pipeline.Step method)

get_output_paths_to_download_when_done() (step_pipeline.pipeline.Step method) get_outputs() (step_pipeline.pipeline.Step method) get_subdir_name() (step_pipeline.io.Localize method) GoogleStorageException GSUTIL_COPY (step_pipeline.io.Delocalize attribute) (step_pipeline.io.Localize attribute)

H

HAIL_BATCH_CLOUDFUSE (step_pipeline.io.Localize attribute) HAIL_BATCH_CLOUDFUSE_VIA_TEMP_BUCKET (step_pipeline.io.Localize attribute) HAIL_BATCH_LOCAL (step_pipeline.constants.Backend attribute), [1]

HAIL_BATCH_SERVICE (step_pipeline.constants.Backend attribute), [1] HAIL_HADOOP_COPY (step_pipeline.io.Delocalize attribute) (step_pipeline.io.Localize attribute) has_upstream_steps() (step_pipeline.pipeline.Step method)

I

input() (step_pipeline.pipeline.Step method) input_glob() (step_pipeline.pipeline.Step method) input_type (step_pipeline.io.InputValueSpec property) input_value() (step_pipeline.pipeline.Step method) inputs() (step_pipeline.pipeline.Step method)

InputSpec (class in step_pipeline.io) InputSpecBase (class in step_pipeline.io) InputType (class in step_pipeline.io) InputValueSpec (class in step_pipeline.io) INT (step_pipeline.io.InputType attribute)

L

local_dir (step_pipeline.io.InputSpec property) (step_pipeline.io.OutputSpec property) local_path (step_pipeline.io.InputSpec property) (step_pipeline.io.OutputSpec property)

localization_root_dir (step_pipeline.io.InputSpec property) Localize (class in step_pipeline.io) localize_by (step_pipeline.io.InputSpec property)

M

memory() (step_pipeline.batch.BatchStep method) (step_pipeline.wdl.WdlStep method) module step_pipeline step_pipeline.batch step_pipeline.constants step_pipeline.io step_pipeline.main step_pipeline.pipeline step_pipeline.utils step_pipeline.wdl

N

name (step_pipeline.io.InputSpecBase property) (step_pipeline.io.OutputSpec property) name() (step_pipeline.pipeline.Step method)

new_step() (step_pipeline.batch.BatchPipeline method) (step_pipeline.pipeline.Pipeline method) (step_pipeline.wdl.WdlPipeline method)

O

optional (step_pipeline.io.OutputSpec property) original_source_path (step_pipeline.io.InputSpec property) output() (step_pipeline.pipeline.Step method) output_dir (step_pipeline.io.OutputSpec property)

output_dir() (step_pipeline.pipeline.Step method) output_path (step_pipeline.io.OutputSpec property) output_path_including_any_wildcards (step_pipeline.io.OutputSpec property) outputs() (step_pipeline.pipeline.Step method) OutputSpec (class in step_pipeline.io)

P

parse_args() (step_pipeline.pipeline.Pipeline method) parse_known_args() (step_pipeline.pipeline.Pipeline method) Pipeline (class in step_pipeline.pipeline) pipeline() (in module step_pipeline.main)

post_to_slack() (step_pipeline.pipeline.Step method) precache_file_paths() (step_pipeline.pipeline.Pipeline method) preemptible() (step_pipeline.batch.BatchStep method) PYTHON (step_pipeline.batch.BatchStepType attribute)

R

record_memory_cpu_and_disk_usage() (step_pipeline.pipeline.Step method) regions() (step_pipeline.batch.BatchStep method) run() (step_pipeline.batch.BatchPipeline method) (step_pipeline.pipeline.Pipeline method) (step_pipeline.wdl.WdlPipeline method)

run_for_each_row() (step_pipeline.wdl.WdlPipeline method)

S

set_name() (step_pipeline.pipeline.Pipeline method) set_storage_to_fit_all_inputs() (step_pipeline.batch.BatchStep method) skip() (step_pipeline.pipeline.Step method) source_bucket (step_pipeline.io.InputSpec property) source_dir (step_pipeline.io.InputSpec property) source_path (step_pipeline.io.InputSpec property) source_path_without_protocol (step_pipeline.io.InputSpec property) Step (class in step_pipeline.pipeline) step_pipeline module step_pipeline.batch module step_pipeline.constants module

step_pipeline.io module step_pipeline.main module step_pipeline.pipeline module step_pipeline.utils module step_pipeline.wdl module storage() (step_pipeline.batch.BatchStep method) (step_pipeline.wdl.WdlStep method) STRING (step_pipeline.io.InputType attribute) switch_gcloud_auth_to_user_account() (step_pipeline.pipeline.Step method)

T

TERRA (step_pipeline.constants.Backend attribute), [1]

timeout() (step_pipeline.batch.BatchStep method)

U

use_previous_step_outputs_as_inputs() (step_pipeline.pipeline.Step method)

use_the_same_inputs_as() (step_pipeline.pipeline.Step method) uuid (step_pipeline.io.InputSpecBase property)

V

value (step_pipeline.io.InputValueSpec property)

W

WdlPipeline (class in step_pipeline.wdl)

WdlStep (class in step_pipeline.wdl)