Index

A

add_to_parser() (OptionEatAll method)

all_extensions (FileFactory property)

B

basenames (FileFactory property)

C

check_input_files() (SequanaManager method) clean_multiqc() (PipelineManagerBase method) ClickFeatureCountsOptions (class in sequana_pipetools.options) ClickGeneralOptions (class in sequana_pipetools.options)

ClickInputOptions (class in sequana_pipetools.options) ClickKrakenOptions (class in sequana_pipetools.options) ClickSlurmOptions (class in sequana_pipetools.options) ClickSnakemakeOptions (class in sequana_pipetools.options) ClickTrimmingOptions (class in sequana_pipetools.options)

D

deps_callback() (ClickGeneralOptions static method)

E

error() (PipelineManagerBase method)

exists() (SequanaManager method) extensions (FileFactory property)

F

FastQFactory (class in sequana_pipetools.snaketools.file_factory) FileFactory (class in sequana_pipetools.snaketools.file_factory)

filenames (FileFactory property) fill_data_options() (SequanaManager method) from_project_callback() (ClickGeneralOptions static method)

G

get_file1() (FastQFactory method) get_file2() (FastQFactory method) get_html_summary() (PipelineManagerBase method) getmetadata() (PipelineManagerBase method) getrawdata() (PipelineManager method) (PipelineManagerBase method)

group_name (ClickFeatureCountsOptions attribute) (ClickGeneralOptions attribute) (ClickInputOptions attribute) (ClickKrakenOptions attribute) (ClickSlurmOptions attribute) (ClickSnakemakeOptions attribute) (ClickTrimmingOptions attribute)

I

include_options_from() (in module sequana_pipetools.options)

init_click() (in module sequana_pipetools.options)

M

metadata (ClickFeatureCountsOptions attribute) (ClickGeneralOptions attribute) (ClickInputOptions attribute) (ClickKrakenOptions attribute) (ClickSlurmOptions attribute) (ClickSnakemakeOptions attribute) (ClickTrimmingOptions attribute)

module sequana_pipetools.options sequana_pipetools.sequana_manager sequana_pipetools.snaketools.file_factory sequana_pipetools.snaketools.pipeline_manager multiple_downloads() (in module sequana_pipetools.sequana_manager)

O

onerror() (PipelineManagerBase method)

OptionEatAll (class in sequana_pipetools.options)

P

paired (FastQFactory property) (PipelineManager property)

PipelineManager (class in sequana_pipetools.snaketools.pipeline_manager) PipelineManagerBase (class in sequana_pipetools.snaketools.pipeline_manager) PipelineManagerDirectory (class in sequana_pipetools.snaketools.pipeline_manager)

R

realpaths (FileFactory property)

S

sequana_pipetools.options module sequana_pipetools.sequana_manager module sequana_pipetools.snaketools.file_factory module

sequana_pipetools.snaketools.pipeline_manager module SequanaManager (class in sequana_pipetools.sequana_manager) setup() (PipelineManagerBase method) (SequanaManager method) snakefile (PipelineManagerBase property)

T

teardown() (PipelineManagerBase method) (SequanaManager method)

V

version_callback() (ClickGeneralOptions static method)