v1.18.0

• Update to latest version of plugin (multiqcv1.14_plugin_v1.4.0.tar.gz)
• Update instance type to mem1_ssd1_v2_x4
• Gene coverage now displayed on reports (Sambamba_chanjo)

v1.17.0

• Update to latest version of plugin (multiqcv1.14_plugin_v1.3.0.tar.gz)
• Allows bclconvert data to be displayed correctly
• Fix recursive QC download to include recursive download of subfolders

update to latest plugin version (v1.2.0) which includes update to multiqc v1.13

• Move from pulling docker image from dockerhub to downloading from 001_Tools
• Update to seglh/multiqc_v1.13:v1.2.0

Add SELGH plugins for som.py, exome depth and TSO500

incorporates SEGLH multiQC plugin v1.0.0 and uses dockerised build in that repo (pulling from dockerhub)
Also adds support for bclconvert (In TSO runs) by recursively downloading the QC folder.
Remove the manipulation of senteion reports due to native support

DNAnexus app v1.14.0 (MultiQC v1.11)

Multiqc.tar.gz file contains the repository contents including the tarred docker image (not in the repository as file size exceeded github's limit)

• Version of multiqc updated to v1.11 from v1.10.1
• Now displays peddy relatedness plot an illumina lane metrics plots for runfolders where that tool's data is present
• Exclusion of gatk from report removed (this module no longer breaks multiqc)
• Change to using tarred/zipped docker image rather than pulling the docker image when it runs - reduces risk of app failing due to connectivity issues/issues with the repo
• Docker image created using dockerfile in repository - fixes issues with official docker image (some modules in multiqc break when using official image)
• Execution environment updated to Ubuntu 20.04

MulitQC version updated to v1.10.1

Updated MultiQC docker version to v1.10.1.
The app now pulls the docker image everytime it runs.
Removed convert_mapping_metrics.py- no longer used MultiQC supports Sentieon outputs now
Jinja dependency removed from dxapp.json as its no longer required.
Ubuntu updated from 14.4 to 16.4

Add support for senteion made apps

Senteion made apps name the duplication files differently (capitalised) so these were not detected by previous versions of this app.

Add conditional formatting to contamination in general stats

Contamination (freemix) highlighted red if >2%

no longer package up api key in app

Merge pull request #30 from moka-guys/v1.10

update to use auth token from 001 project

Fix issue so doesn't error on non-WES runs

Merge pull request #28 from moka-guys/v1.9

work properly with custom panels