Implement WGS structural variant calling pipeline

[Nicklas Nordborg]

This should be similar to the existing WGS variant calling, but check for structural variants instead. gridss (​https://github.com/PapenfussLab/gridss) is a possible candidate to use for the variant calling, but we probably need some post processing of the results as well.

[Nicklas Nordborg]

In 7924:

References #1623: Implement WGS structural variant calling pipeline

Added an item list, pipeline and annotation type category for structural variant calls. New wizards on the start page.

[Nicklas Nordborg]

In 7925:

References #1623: Implement WGS structural variant calling pipeline

Started to implement this wizard. Tumor-Normal pairs can be selected and submitted to the cluster but the script doesn't do anything.

[Nicklas Nordborg]

In 7926:

References #1623: Implement WGS structural variant calling pipeline

Added a container with gridss.

[Nicklas Nordborg]

In 7927:

References #1623: Implement WGS structural variant calling pipeline

Started to implement the variant calling script. First step is to copy the tumor and normal BAM files. In debug mode it is possible to work with a subset (chr1 default).

[Nicklas Nordborg]

In 7928:

References #1623: Implement WGS structural variant calling pipeline

Added the gridss pre-processing step.