Per Unneberg

Have tasks talk to a central planner so task lists can be easily monitored via a web page. Start out with gandalf.

Implement class validation of parent_task. Currently, any code can be used, but it would be nice if the class be validated against the parent class, for instance by using interfaces

Add 'target_grouping' or something similar to BaseJobTask to use for grouping in table output.

Modules server.py, the subdirectory static, and the daemon are more or less copies from luigi.

Instead of bwaref etc for setting alignment references, utilise cloudbiolinux/tool-data

Check for program versions and command inconsistencies: for instance, BaseRecalibrator was introduced in GATK 2.0. EDIT: I'm thinking it's best not to elaborate too much on this part, but leave...

Currently need to know target name. Add function that prints in which order labels are added to facilitate target name construction. Basically we need to gather all labels between two...

UPSTREAM in ratatosk.job.DefaultShellJobRunner._fix_paths, a.move(b) doesn't work (I modelled this after luigi hadoop_jar)

**Snakemake version** v8 **Describe the bug** Missing conda/mamba in snakemake docker image. From v8 (?) parent image is mambaorg/micromamba which uses micromamba but does not ship conda/mamba executables by default...

The function `GFF.parse` has the option `base_dict` that is a dictionary of SeqRecord object to which gff entries are added upon parsing. If `base_dict` is an `OrderedDict` (default in newer...