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bioluigi's Issues

Add a recursive reenable command to the CLI

In case of a disabled task, this re enables the task for being scheduled at a later point.

In the case of upstream disabled task, it is useful to re enable the dependencies recursively.

bioluigi reenable [--recursive] TASK_ID

Add a target type for indexed luigi.LocalTarget

This would apply to indexed BAMs and VCFs and possibly other tabular format with tabix. This would basically turn the folowwing:

class TaskThatProducesIndexedOutput(luigi.Task):
    def output(self):
        return luigi.LocalTarget('test.vcf.gz'), luigi.LocalTarget('test.vcf.tbi.gz')

Into:

class TaskThatProducesIndexedOutput(luigi.Task):
    def output(self):
        return bioluigi.targets.IndexedLocalTarget('test.vcf.gz')

It would be considered complete if both resulting local targets exist.

AttributeError when formatting a None object in TooManyTaskError message 

Traceback (most recent call last):
  File "/space/grp/poirigui/miniconda3/envs/rnaseq-pipeline/lib/python3.9/site-packages/bioluigi/cli.py", line 151, in list
    tasks.update(rpc(scheduler_url, 'task_list', search=search, limit=limit))
  File "/space/grp/poirigui/miniconda3/envs/rnaseq-pipeline/lib/python3.9/site-packages/bioluigi/cli.py", line 28, in rpc
    raise TooManyTasksError(response_data['num_tasks'])
bioluigi.cli.TooManyTasksError: <exception str() failed>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/space/grp/poirigui/miniconda3/envs/rnaseq-pipeline/bin/bioluigi", line 8, in <module>
    sys.exit(main())
  File "/space/grp/poirigui/miniconda3/envs/rnaseq-pipeline/lib/python3.9/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/space/grp/poirigui/miniconda3/envs/rnaseq-pipeline/lib/python3.9/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/space/grp/poirigui/miniconda3/envs/rnaseq-pipeline/lib/python3.9/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/space/grp/poirigui/miniconda3/envs/rnaseq-pipeline/lib/python3.9/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/space/grp/poirigui/miniconda3/envs/rnaseq-pipeline/lib/python3.9/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/space/grp/poirigui/miniconda3/envs/rnaseq-pipeline/lib/python3.9/site-packages/click/decorators.py", line 26, in new_func
    return f(get_current_context(), *args, **kwargs)
  File "/space/grp/poirigui/miniconda3/envs/rnaseq-pipeline/lib/python3.9/site-packages/bioluigi/cli.py", line 153, in list
    click.echo(e, err=True)
  File "/space/grp/poirigui/miniconda3/envs/rnaseq-pipeline/lib/python3.9/site-packages/click/utils.py", line 258, in echo
    out: t.Optional[t.Union[str, bytes]] = str(message)
  File "/space/grp/poirigui/miniconda3/envs/rnaseq-pipeline/lib/python3.9/site-packages/bioluigi/cli.py", line 19, in __str__
    return 'That request would return {} tasks; try filtering by status, glob query or set the --no-limit flag.'.format(format_number(self.num_tasks) if self.num_tasks else 'an unknown amount of')
  File "/space/grp/poirigui/miniconda3/envs/rnaseq-pipeline/lib/python3.9/site-packages/babel/numbers.py", line 353, in format_number
    return format_decimal(number, locale=locale)
  File "/space/grp/poirigui/miniconda3/envs/rnaseq-pipeline/lib/python3.9/site-packages/babel/numbers.py", line 419, in format_decimal
    format = locale.decimal_formats.get(format)
AttributeError: 'NoneType' object has no attribute 'decimal_formats'

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