Index

Symbols

.snakemake

_

__getitem__() (ObjectGraph method)

A

add() (ObjectGraph method)

add_targets() (in module snakeobjects.snakeUtils)

B

build_object_graph (DirectoryPipeline attribute) (PackagePipeline attribute) build_object_graph.py

buildObjectGraph sobjects command line option built-in function run()

C

cleanProject sobjects command line option createSnakefile sobjects command line option

createSymbolicLinks sobjects command line option

D

definition_dir (DirectoryPipeline attribute) definition_package (PackagePipeline attribute) deps (OGO attribute) describe sobjects command line option

directory (Project attribute) DirectoryPipeline (class in snakeobjects.Project) DP() (in module snakeobjects.snakeUtils) DT() (in module snakeobjects.snakeUtils)

E

EF() (in module snakeobjects.snakeUtils)

environment.yaml

F

find_so_project_directory() (in module snakeobjects.Project)

G

get_definition() (DirectoryPipeline method) (PackagePipeline method) (Pipeline method) get_environment_variables (DirectoryPipeline attribute) (PackagePipeline attribute) get_main_snakefile_path (DirectoryPipeline attribute) (PackagePipeline attribute) get_object_directory (Project attribute)

get_object_path (Project attribute) get_object_types() (ObjectGraph method) get_parameter (Project attribute) get_pipeline_directory (Project attribute) get_snakefile_directory (DirectoryPipeline attribute) (PackagePipeline attribute) graph sobjects command line option

H

help sobjects command line option

J

jobscript.sh

L

LFS() (in module snakeobjects.snakeUtils)

load_object_graph() (in module snakeobjects)

M

metadata module snakeobjects snakeobjects.snakeUtils

O

object object graph object name object type object's parameters

ObjectGraph (class in snakeobjects) objectGraph (Project attribute) OG.json OGO (class in snakeobjects.ObjectGraph) oId (OGO attribute) oType (OGO attribute)

P

P() (in module snakeobjects.snakeUtils) PackagePipeline (class in snakeobjects.Project) parameters (Project attribute) params (OGO attribute) parent_projects (Project attribute) pipeline Pipeline (class in snakeobjects.Project) PP() (in module snakeobjects.snakeUtils)

prepare sobjects command line option prepareTest sobjects command line option printEnv sobjects command line option project Project (class in snakeobjects) project parameters

R

run sobjects command line option

run() built-in function

S

save() (ObjectGraph method) snake_file_dir (PackagePipeline attribute) Snakefile snakefile_directory (DirectoryPipeline attribute) snakeobjects module snakeobjects.snakeUtils module so_project.yaml sobjects command line option buildObjectGraph cleanProject createSnakefile createSymbolicLinks describe graph help prepare prepareTest printEnv run submit version

sobjects commands submit sobjects command line option

T

T() (in module snakeobjects.snakeUtils)

target TE() (in module snakeobjects.snakeUtils)

V

version sobjects command line option