Formatting and minor cleanups

Author: arteymix

bioluigi/config.py

@@ -1,11 +1,11 @@
 import luigi
 
 class bioluigi(luigi.Config):
-    scheduler = luigi.Parameter(default='local', significant=False,
+    scheduler = luigi.Parameter(default='local',
                                 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,
+    scheduler_partition = luigi.OptionalParameter(default=None,
+                                                  description='Partition (or queue) to use for scheduling jobs if supported by the scheduler')
+    scheduler_extra_args = luigi.ListParameter(default=[],
                                                description='List of extra arguments to pass to the scheduler')
     prefetch_bin = luigi.Parameter(default='prefetch')
     fastqdump_bin = luigi.Parameter(default='fastq-dump')
@@ -15,7 +15,7 @@ class bioluigi(luigi.Config):
     rsem_dir = luigi.Parameter(default='')
     bcftools_bin = luigi.Parameter(default='bcftools')
     vep_bin = luigi.Parameter(default='vep')
-    vep_dir = luigi.OptionalParameter(default='', significant=False)
+    vep_dir = luigi.OptionalParameter(default=None)
     multiqc_bin = luigi.Parameter(default='multiqc')
     cellranger_bin = luigi.Parameter(default='cellranger')
     bamtofastq_bin = luigi.Parameter(default='bamtofastq')

bioluigi/scheduled_external_program.py

@@ -27,7 +27,8 @@ class ScheduledExternalProgramTask(ExternalProgramTask, ScheduledTask):
     Variant of :class:`luigi.contrib.external_program.ExternalProgramTask` that
     executes the task with a :class:`Scheduler`.
     """
-    scheduler: str = luigi.ChoiceParameter(default=cfg.scheduler, choices=['local'] + [blurb for blurb in get_available_schedulers()],
+    scheduler: str = luigi.ChoiceParameter(default=cfg.scheduler,
+                                           choices=['local'] + [blurb for blurb in get_available_schedulers()],
                                            positional=False, significant=False,
                                            description='Scheduler to use for running the task')
     scheduler_partition: Optional[str] = luigi.OptionalParameter(default=cfg.scheduler_partition, positional=False,

bioluigi/schedulers.py

@@ -1,12 +1,11 @@
+import json
 import logging
-from abc import abstractmethod, ABC, abstractclassmethod
+from abc import abstractmethod, ABC
 from datetime import timedelta
 from subprocess import Popen, PIPE
-import json
 from typing import Optional
 
 import luigi
-
 from luigi.contrib.external_program import ExternalProgramRunError, ExternalProgramRunContext
 
 logger = logging.getLogger(__name__)

bioluigi/tasks/bcftools.py

@@ -191,7 +191,7 @@ class Merge(BcftoolsTask):
     output_file: str = luigi.Parameter()
     output_format: str = luigi.Parameter(positional=False, default='z')
 
-    _tmp_output_file : str = None
+    _tmp_output_file: str = None
 
     def subcommand_args(self):
         args = ['merge']

bioluigi/tasks/fastqc.py

@@ -1,4 +1,3 @@
-import os
 from os import makedirs
 from os.path import join, basename, splitext
 from typing import Optional

bioluigi/tasks/sratoolkit.py

@@ -1,5 +1,5 @@
 from os.path import join, basename, splitext
-from typing import Optional, SupportsIndex
+from typing import Optional
 
 import luigi