Support TSO dry lab model

• TSO runs no longer tarred before uploading to DNAnexus. Entire run is uploaded including BCL files
• Updated TSO app and tso_output_parser app versions
• Provided dnanexus user id to give user access to TSO runs.
• Updated MultiQC version
• Updated Mokapipe version (inew pipeline included polyedge app for MSH2)

change VCP3 BED file

Change BED file used for VCP3 (4535->4995)

Add support for TSO500 high throughput

Pan numbers extracted from samplenames in consistent way
Lay the foundation for wet/dry lab model for TSO
Allow instance type to be specified for TSO based on Pan number

Add support for extra pan numbers

Merge pull request #427 from moka-guys/v44.3.4

add support for mike mitchels' pan numbers

Mokapipe v2.16

mokapipe updated to v2.16 (inclusion of bcftools stats)
congenica SFTP upload app
mokapipe dx run commands allows for the capture type to be given to picard
minor formatting changes

Add support for github actions applying linter

stop the build if there are Python syntax errors or undefined names
flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics

fix missing comma in config

Merge pull request #416 from moka-guys/v43.3.1

missing comma

Add support for LRPCR

Add support for LRPCR - provide masked reference genome to BWA
Allow TSO tar step to be repeated once
Change timeout policy to GATK app where it's an FH sample
remove onepgt function

Update TSO500 apps and BED file, includes running sompy

Updates the TSO500 apps to TSO500_v1.4.0 and TSO500_output_parser_v1.2.0 and updates the TSO500 coverage BED file

Update snpgenotyping to mokaSNP_v1.2.0

Merge pull request #399 from moka-guys/v44.1.0

V44.1.0