2.8.0.

Using nextflow research pipeline

• added arguments to use the research tool/workflow also as input for the PGx-pipeline

2.7.0.

Implemented new system for new diagnostics clusters (beta barrel and copperfist)
Update Jenkinsfile/automated testing of changes in the array repo
Updated python scripts to python 3
Updated dependencies to newer versions with newer toolchains
fixed shellcheck

2.6.0

What's Changed

• Improved logging and added \r, so lines wrap correctly in email to GD colleagues, who are on Windows machines.
• Update Jenkinsfile
• removed unused protocols and scripts and edited workflow for research
• fixed shellcheck
• added CheckRawDataOnTmp step for new diagnostic clusters

2.5.0

This release contains multiple updates for the diagnostics workflow:

• Fixed shellcheck errors
• Updates for emailing when gender does not match the sampleID column of the samplesheet
• Updates for working and emailing when samples are missing
• Removed large step which creates a report for UPD analysis (UPD analysis wil be performed using NxClinical)
• Calculating standard deviation on different file format (SD calculation itself has not changed)

2.3.1

Tekst komt later

v2.2.1

• Several bugfixes
• Making copyPrmToTmp easier and quicker
• Updated start-pipeline to prevent crashes
• Remove double loop

v2.2.0

Diagnostics:

Implemented+update Concordance Check Script in diagnostics workflow
Script for archiving VCF's in concordance folder when older then certain time
Script for archiving Concordance results to prm dir
Research

Implementation of autosomal + genotype QC step
Making final reports per array slide
Merging all final reports

v2.0.1

• Removed Concordance protocol from workflow

v2.0.0

New scripts:

• Added protocol to workflow for making concordance input

Bugfixes:

• Diagnostics output .finished file moved to diagnosticsoutput/${project folder}/
• Fixed version number in generate template.

v1.0.1

updated .bpm file for processing GSA-MD chips.