Index

_ | A | F | I | L | M | O | P | R | S | T | W

_

_fill_adapters() (rnaseqflow.cliutils.ArgFiller method)
_fill_blocksize() (rnaseqflow.cliutils.ArgFiller method)
_fill_ext() (rnaseqflow.cliutils.ArgFiller method)
_fill_fastq() (rnaseqflow.cliutils.ArgFiller method)
_fill_fastq_args() (rnaseqflow.cliutils.ArgFiller method)
_fill_quiet() (rnaseqflow.cliutils.ArgFiller method)
_fill_root() (rnaseqflow.cliutils.ArgFiller method)
_find_file_pairs() (rnaseqflow.workflow.FastQMCFTrimPairs method)
_get_direction_id() (rnaseqflow.workflow.MergeSplitFiles static method)
_get_directory_input() (rnaseqflow.cliutils.ArgFiller class method)
_get_filepath_input() (rnaseqflow.cliutils.ArgFiller class method)
_get_integer_input() (rnaseqflow.cliutils.ArgFiller class method)
_get_part_num() (rnaseqflow.workflow.MergeSplitFiles static method)
_get_sequence_id() (rnaseqflow.workflow.FastQMCFTrimPairs static method)
(rnaseqflow.workflow.MergeSplitFiles static method)
_organize_files() (rnaseqflow.workflow.MergeSplitFiles method)

A

all_subclasses() (in module rnaseqflow.cliutils)
append() (rnaseqflow.workflow.Workflow method)
ArgFiller (class in rnaseqflow.cliutils)

F

FastQMCFTrimPairs (class in rnaseqflow.workflow)
FastQMCFTrimSolo (class in rnaseqflow.workflow)
fill() (rnaseqflow.cliutils.ArgFiller method)
FindFiles (class in rnaseqflow.workflow)
firstline() (in module rnaseqflow.cliutils)

I

insert() (rnaseqflow.workflow.Workflow method)

L

logger (rnaseqflow.workflow.FastQMCFTrimPairs attribute)
(rnaseqflow.workflow.FastQMCFTrimSolo attribute)
(rnaseqflow.workflow.FindFiles attribute)
(rnaseqflow.workflow.MergeSplitFiles attribute)
(rnaseqflow.workflow.Workflow attribute)
(rnaseqflow.workflow.WorkflowStage attribute)
longhelp() (rnaseqflow.workflow.WorkflowStage class method)

M

main() (in module rnaseqflow.__main__)
MergeSplitFiles (class in rnaseqflow.workflow)

O

opts() (in module rnaseqflow.__main__)

P

pathCompleter() (rnaseqflow.cliutils.ArgFiller method)
Python Enhancement Proposals
PEP 0257, [1]
PEP 0257#handling-docstring-indentation

R

run() (rnaseqflow.workflow.FastQMCFTrimPairs method)
(rnaseqflow.workflow.FastQMCFTrimSolo method)
(rnaseqflow.workflow.FindFiles method)
(rnaseqflow.workflow.MergeSplitFiles method)
(rnaseqflow.workflow.Workflow method)
(rnaseqflow.workflow.WorkflowStage method)

S

set_path_complete() (rnaseqflow.cliutils.ArgFiller method)
shorthelp() (rnaseqflow.workflow.WorkflowStage class method)
spec (rnaseqflow.workflow.FastQMCFTrimPairs attribute)
(rnaseqflow.workflow.FastQMCFTrimSolo attribute)
(rnaseqflow.workflow.FindFiles attribute)
(rnaseqflow.workflow.MergeSplitFiles attribute)
(rnaseqflow.workflow.WorkflowStage attribute)

T

trim() (in module rnaseqflow.cliutils)

W

Workflow (class in rnaseqflow.workflow)
WorkflowStage (class in rnaseqflow.workflow)