Index

Symbols

.snakemake

_

__getitem__() (ObjectGraph method)

A

add() (ObjectGraph method)

add_targets() (in module snakeobjects.snakeUtils)

B

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

deps (OGO attribute) describe sobjects command line option

directory (Project attribute) 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_object_directory (Project attribute) get_object_path (Project attribute) get_object_types() (ObjectGraph method)

get_parameter (Project attribute) get_pipeline_directory (Project 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) parameters (Project attribute) params (OGO attribute) parent_projects (Project attribute) pipeline 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) Snakefile 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