mokapipe v2.15 and more

Mokapipe version updated to v2.15 - this includes the FH_PRS app (v1.0.2), sambamba/chanjo app v1.13 and vcf_eval v1.4.1.
New Pan numbers for TSO (updated BED file), R259 and EB samples.
WES_EB samples can now be uploaded in the using the congenica upload app (now v1.3.2)
Some small changes to make the script more robust have been added so it shouldn't fail if certain steps fail, eg failure to send emails.
the VCP2 bedfiles have been changed to include all of CHEK2
All workflows are now set off as high priority to ensure they are not affected by use of spot instances.

turn back on tar TSO500 runfolder function

Merge pull request #391 from moka-guys/v43.0.4

uncomment tar runfolder function

Disable smartsheet run command

V43.0.3 caused issues with the generation of the email with the SQL queries and the complete upload of run folders.
The scripts have been updated to fix these issues by removing False statements from try and except statements added in v43.0.3
The dx run commands for the SmartSheet have been commented out.

fixes the error with Smartsheet API

Added try and except statements added to demultiplex.py and upload_and_setoff_workflows.py to stop scripts from failing.

v43.0.2

Upgrade to multiqc v1.15.0 (supports SEGLH multiqc plug in v1.0.0 (https://github.com/moka-guys/multiqc_plugins/tree/v1.0.0))
Fixed the dx run command for TSO app
Add SQL audit trail email for TSO
Slight changes to the way email body is built.
Add recipients to samplename email

fixes to TSO500 automation

TSO runfolder tarball created properly.
TSO500 app v1.3
New Pan number for TSO used.
TSO500 specific samplesheet requirements added.
Expected runfolder naming defined as starting with 6 digits so samplesheet validator doesn't trigger alerts for non-runfolder dirs

fully support TSO500, samplesheet verifier

Set off TSO500 and TSO500_output parser apps
Samplesheet verifier acts as early warning system for samplesheet issues
Samplesheets are now uploaded again
Logfile check is working as expected.
Additional Pan numbers created for each R number for STG

TSO500 tar and upload. MokaAMP v2.2

renamed test runfolders.
MokaAMP v2.2
For TSO500 skip demultiplexing, create tar and upload tar.
docker command for lane density has --rm added

v41.1.0

• Update to mokaampv2.2
• Update to mokapipev2.13 (includes removal of variant annotator and addition of filter_vcf_with_bedfile v1.0)
• Update multiqc to v1.14.0

v41.0.0

Update to use MokaAMPv2.1 and remove MokaONC