bioluigi package

Subpackages

• bioluigi.tasks package
  • Submodules
  • bioluigi.tasks.bcftools module
  • bioluigi.tasks.cutadapt module
  • bioluigi.tasks.fastqc module
  • bioluigi.tasks.gatk module
  • bioluigi.tasks.multiqc module
  • bioluigi.tasks.rsem module
  • bioluigi.tasks.samtools module
  • bioluigi.tasks.sratoolkit module
  • bioluigi.tasks.star module
  • bioluigi.tasks.utils module
    • CreateTaskOutputDirectoriesBeforeRunMixin
      • CreateTaskOutputDirectoriesBeforeRunMixin.run()
    • DynamicTaskWithOutputMixin
      • DynamicTaskWithOutputMixin.output()
      • DynamicTaskWithOutputMixin.unpack_singleton
    • DynamicWrapperTask
      • DynamicWrapperTask.complete()
    • RemoveTaskOutputOnFailureMixin
      • RemoveTaskOutputOnFailureMixin.on_failure()
    • TaskWithMetadataMixin
      • TaskWithMetadataMixin.metadata
    • TaskWithOutputMixin
      • TaskWithOutputMixin.output()
  • bioluigi.tasks.vep module
  • Module contents

Submodules

bioluigi.cli module

bioluigi.config module

class bioluigi.config.BioluigiConfig(*args, **kwargs)

Bases: Config

Bioluigi configuration

bamtofastq_bin = Parameter (defaults to bamtofastq)

bcftools_bin = Parameter (defaults to bcftools)

cellranger_bin = Parameter (defaults to cellranger)

cutadapt_bin = Parameter (defaults to cutadapt)

fastqc_bin = Parameter (defaults to fastqc)

fastqdump_bin = Parameter (defaults to fastq-dump)

classmethod get_task_family()

The task family for the given class.

If task_namespace is not set, then it’s simply the name of the class. Otherwise, <task_namespace>. is prefixed to the class name.

Note: You normally don’t want to override this.

multiqc_bin = Parameter (defaults to multiqc)

prefetch_bin = Parameter (defaults to prefetch)

rsem_dir = Parameter (defaults to )

samtools_bin = Parameter (defaults to samtools)

scheduler = Parameter (defaults to local): Default scheduler to use in ScheduledExternalProgram

scheduler_extra_args = ListParameter (defaults to []): List of extra arguments to pass to the scheduler

scheduler_partition = OptionalParameter (defaults to None): Partition (or queue) to use for scheduling jobs if supported by the scheduler

star_bin = Parameter (defaults to STAR)

vep_bin = Parameter (defaults to vep)

vep_dir = OptionalParameter (defaults to None)

bioluigi.config.bioluigi

Kept for backward-compatibility, use BioluigiConfig instead

bioluigi.scheduled_external_program module

Module contents