v33

Add SQL queries to record pipeline version for cancer
Add runid to mokapipe queries
Modify decision support tool input script to upload to IVA
Fix errors with checking for successful uploads

v32

MokaAMP upgraded from 1.3 -> 1.4
Upload MultiQC upgraded from 1.1 to 1.2 (uploads trend analysis data to server)
use RPKM using conifer v1.6
Add support for VCP panels
Calculates Illumina lane metrics
Multiqc does not start before Peddy finishes
Fix error which lead to log files not being uploaded

v31

Restrict variant calling for STG BRCA samples - this requires a new Pan number
Stop automated upload to Sapientia - these commands are written to a bash file which can be executed once QC check passed. A slack alert has been added
Upgrade to MokaAMP_v1.3 - this includes ingenuity import
Turn of MokaAMP for Pan1190, as this would result in 2x VCFS in Ingenuity
Fixed issue to ensure the rest of runfolder completes successfully (and alert issued if error raised)

Major refactor

This release is a major refactor of these scripts.
Two new scripts have been created (adlogger and decision_support_tool_input). These perform logging functions and are run when the dx run commands are set off.

The upload_agent.py script has been renamed, and refactored to:

• be more amenable to unit tests.
• support multiple decision support tools (for mokapipe) - utilising decision_support_tool_inputs.py
• Use a new version of RPKM app (v1.5) which supports the joint analysis of multiple pan numbers.
• Panel specific settings are now in the config file, rather than hardcoded in the script. This dictionary allows easy addition of pan numbers and lots of flexibility when issuing dx run commands.
• This also supports the new MokaAMP pipeline, and should be easier to add further pipelines in the future.
  -Log files are now written using the python logger module, using the ADlogger script.
• The backup.py script is used to upload the rest of the run folder.
• mokapipe updated to v2.12
• mokawes updated to v1.8
• mokaamp updated to v1.2
• Peddy to v1.5
• multiqc to v1.12
• sapientia upload tool v1.0
• rpkm_using_conifer_v1.5
• smartsheet_update_v1.2

The following panels are supported:
Pan493,Pan1063,Pan1190,Pan2684,Pan1440,Pan2022,Pan1965,Pan1158,Pan1159,Pan1646,Pan3320,Pan2835

Minor changes were made to the demultiplexing script - this should be made more OO and amenable to unit testing at a later stage.

v29

MokaWESv1.7
Updated config file to reflect changes in the stages of the pipeline
Changed pipeline_ID to reflect MokaWESv1.7

v28

Can be run multiple times per hour
Uses --name to name analyses
Mokapipe v2.10
multiqc v1.11
mokaamp v1.3
uploads underdetermined fastq files

Config points to share on new hard drive

Installed new hard drive to increase capacity. The config was updated to point to the new share.

Integrity check on any sequencer name stated in config

MokaAMP upgrade from v1.0 to v1.1

Use MokaWES v1.5

Merge pull request #237 from woook/v25

Update to use mokawes v1.5

Bug fixes, use relative file paths

Don't exit if run without samplesheet is found
Remove depends on line following negative control MokaAMP dx run command
Change to relative file paths to allow code to be moved to root instead of home directory