v3.1.1

What's Changed

• Point CGC deploy action to updated repo path by @adthrasher in #27

Full Changelog: v3.1.0...v3.1.1

safety-mode

Partially deactivate parallelism. Applicable to some platforms.

v3.0.9

1. Generates diagnostic error message from indel calling step.
2. Better handles downsamling exceptions at the realignment step.

v3.0.7

Add license and categories to CWL implementation

v3.0.6

CGC CWL and automation

new implementation

A near-complete reimplementation of v2.2.4 using indelPost.

v2.2.4

Minor version bump to align tag names with automations

COSMIC count

COSMIC count is annotated in the output VCF.
Recurrence count is revised to include all somatic predictions.

Python requirement >= 3.6

Python version requirement is updated (from >= 3.5 to >= 3.6).
This is due to build failure of pysam 0.15.4 on 3.5, which has undated cython version.

Target analysis

Allow users to run target analysis by adding option --region chrN:start-pos
sk-learn version requirement updated.