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
- bioluigi.tasks.vep module
- Module contents
Submodules
bioluigi.cli module
bioluigi.config module
- class bioluigi.config.bioluigi(*args, **kwargs)[source]
Bases:
Config- bcftools_bin = Parameter (defaults to bcftools)
- cutadapt_bin = Parameter (defaults to cutadapt)
- fastqc_bin = Parameter (defaults to fastqc)
- fastqdump_bin = Parameter (defaults to fastq-dump)
- multiqc_bin = Parameter (defaults to multiqc)
- prefetch_bin = Parameter (defaults to prefetch)
- rsem_dir = Parameter (defaults to )
- scheduler = Insignificant Parameter (defaults to local): Default scheduler to use in ScheduledExternalProgram
- scheduler_extra_args = Insignificant ListParameter (defaults to []): List of extra arguments to pass to the scheduler
- scheduler_partition = Insignificant OptionalParameter (defaults to ): Node partition to use for scheduling jobs if supported
- star_bin = Parameter (defaults to STAR)
- vep_bin = Parameter (defaults to vep)
- vep_dir = Insignificant OptionalParameter (defaults to )