import luigi
[docs]class bioluigi(luigi.Config):
scheduler = luigi.Parameter(default='local', significant=False, description='Default scheduler to use in ScheduledExternalProgram')
scheduler_partition = luigi.OptionalParameter(default='', significant=False, description='Node partition to use for scheduling jobs if supported')
scheduler_extra_args = luigi.ListParameter(default=[], significant=False, description='List of extra arguments to pass to the scheduler')
prefetch_bin = luigi.Parameter(default='prefetch')
fastqdump_bin = luigi.Parameter(default='fastq-dump')
cutadapt_bin = luigi.Parameter(default='cutadapt')
fastqc_bin = luigi.Parameter(default='fastqc')
star_bin = luigi.Parameter(default='STAR')
rsem_dir = luigi.Parameter(default='')
bcftools_bin = luigi.Parameter(default='bcftools')
vep_bin = luigi.Parameter(default='vep')
vep_dir = luigi.OptionalParameter(default='', significant=False)
multiqc_bin = luigi.Parameter(default='multiqc')