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Identify:

- bootstrap for MAF samples
- How to make bootstrap results compatible with non-bootstrap results
- Limit identify to a subset of signatures
- Create subsets of signatures based on correlation clustering for de-correlation and avoiding collinearity
- Create named signature sets and named subsets
- clustergrammer for reporting and visualization of results of identify/decomposition
- How to output reports?
- rpy2 or reticulate for integration with R reports
- BayesianOptimization for global optimization

- restore functionality of benchmark module

Motifs

+ output motif matches in a separate file
- Motif calibration depending on window size, motif length and the number of mutations
- Comparison of motifs with signatures

Ranking

- Implement ranking of nucleotide mutations from VCF
- Precalculate cohorts
- rank should accept either MAF (or VCF) or precalculated data as input
- Profile, Cohort size and observed mutations is required input. By default they are all coming from the same source
- Define command line use cases
- Rename cohort to data bundle: samples,

Fetch

- test MSKCC
- test GDC
- test ICGC
- consider other sources?
- convert genomes to 2bit
- Autodownloading genome assembly
- Re-enable genome-less version (via ENSEMBL) for testing a limited number of mutations or even a single mutation

General

- Autodection of genome assembly from VCF and MAF
- Upgrade website to use mutagene library
- Accept YAML config file as input for reproducibility
- Create CWL wrappers and dockerized container versions for pipline deployment
- Write a parseable human readable log file containing provisioning information for reproducibility. Should include all parameters, versions / config file that can be used as an input

Tests

+ currently package test suite is failing
- need to make sure we have a CLI test for every function (not every option combination though)
? what other test files can we bundle (licensing issues), perhaps cell lines?

Documentation

* readthedocs documentation
    Example: https://plastid.readthedocs.io/en/latest/quickstart.html

* Improve README
 - main section
 - Installation
 - Changes
 - Documentation
 - Usage (printout of argparse usage)

* Examples:
    - cell lines examples

Links:

- https://github.com/mskcc/vcf2maf
- https://github.com/PoisonAlien/maftools
- https://riptutorial.com/bioinformatics/example/14312/mutation-annotation-format--maf-

- http://docs.h5py.org/en/latest/high/dataset.html#dataset