Index

B

bam_file (bioluigi.tasks.samtools.IndexBam attribute) bcftools_bin (bioluigi.config.bioluigi attribute) bioluigi module bioluigi (class in bioluigi.config) bioluigi.config module

bioluigi.tasks module bioluigi.tasks.gatk module bioluigi.tasks.samtools module bioluigi.tasks.utils module

C

complete() (bioluigi.tasks.utils.DynamicWrapperTask method)

CreateTaskOutputDirectoriesBeforeRunMixin (class in bioluigi.tasks.utils) cutadapt_bin (bioluigi.config.bioluigi attribute)

D

DynamicTaskWithOutputMixin (class in bioluigi.tasks.utils)

DynamicWrapperTask (class in bioluigi.tasks.utils)

F

fastqc_bin (bioluigi.config.bioluigi attribute)

fastqdump_bin (bioluigi.config.bioluigi attribute)

I

IndexBam (class in bioluigi.tasks.samtools)

M

metadata (bioluigi.tasks.utils.TaskWithMetadataMixin attribute) module bioluigi bioluigi.config bioluigi.tasks bioluigi.tasks.gatk bioluigi.tasks.samtools bioluigi.tasks.utils

multiqc_bin (bioluigi.config.bioluigi attribute)

O

on_failure() (bioluigi.tasks.utils.RemoveTaskOutputOnFailureMixin method) output() (bioluigi.tasks.samtools.IndexBam method) (bioluigi.tasks.utils.DynamicTaskWithOutputMixin method) (bioluigi.tasks.utils.TaskWithOutputMixin method)

P

prefetch_bin (bioluigi.config.bioluigi attribute)

program_args() (bioluigi.tasks.samtools.IndexBam method)

R

RemoveTaskOutputOnFailureMixin (class in bioluigi.tasks.utils)

rsem_dir (bioluigi.config.bioluigi attribute) run() (bioluigi.tasks.utils.CreateTaskOutputDirectoriesBeforeRunMixin method)

S

scheduler (bioluigi.config.bioluigi attribute) scheduler_extra_args (bioluigi.config.bioluigi attribute)

scheduler_partition (bioluigi.config.bioluigi attribute) star_bin (bioluigi.config.bioluigi attribute)

T

TaskWithMetadataMixin (class in bioluigi.tasks.utils)

TaskWithOutputMixin (class in bioluigi.tasks.utils)

V

vep_bin (bioluigi.config.bioluigi attribute)

vep_dir (bioluigi.config.bioluigi attribute)