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
- class bioluigi.tasks.samtools.IndexBam(*args, **kwargs)[source]
Bases:
ExternalProgramTask
- bam_file = Parameter
- output()[source]
The output that this Task produces.
The output of the Task determines if the Task needs to be run–the task is considered finished iff the outputs all exist. Subclasses should override this method to return a single
Target
or a list ofTarget
instances.- Implementation note
If running multiple workers, the output must be a resource that is accessible by all workers, such as a DFS or database. Otherwise, workers might compute the same output since they don’t see the work done by other workers.
See Task.output
- program_args()[source]
Override this method to map your task parameters to the program arguments
- Returns:
list to pass as
args
tosubprocess.Popen
bioluigi.tasks.sratoolkit module
bioluigi.tasks.star module
bioluigi.tasks.utils module
Collection of utilities and mixins for tasks
- class bioluigi.tasks.utils.CreateTaskOutputDirectoriesBeforeRunMixin[source]
Bases:
object
Ensures that output directories exist before running the task.
- class bioluigi.tasks.utils.DynamicTaskWithOutputMixin[source]
Bases:
object
Extends a task to forward its dynamic dependencies as output.
- class bioluigi.tasks.utils.DynamicWrapperTask(*args, **kwargs)[source]
Bases:
Task
Similar to luigi.task.WrapperTask but for dynamic dependencies yielded in the body of the run() method.
- class bioluigi.tasks.utils.RemoveTaskOutputOnFailureMixin[source]
Bases:
object
Remove a task outputs on failure.
This only applies for output that have a defined ‘remove’ method.