Per Unneberg

Hi, this probably relates back to #38 which addressed issue #37. The partitions are up, but if you submit the example job to the debug partition, it runs indefinitely, e.g:...

no apparent size reduction of multi-track files as function of no of samples

1

Hi, I'm working on a large genome where we have many samples (~1000). For downstream analyses I need to generate per-base sequence masks based on coverages. To save space, I...

Currently we're setting references, indices etc via functions in a manner that is hidden from the user. All these functions (annotation, index, ref, etc) should be placed in metadata-specific modules...

Make rules independent of snakemakelib package

1

It should be possible to include rules without making use of snakemakelib functionality. We can still set configuration defaults, but they should be general enough to be included without installing...

Interact with module system (see https://github.com/TACC/Lmod). Add configuration variable to list modules that should be loaded.

For quality control settings, basically, allow for a list of expressions with keywords like ">10", "

Basically allow for documentation strings. It is becoming more and more obvious that documentation strings are needed. One solution could be to define configuration entries as 3-tuples of (default, config,...