v3.0.4

• Correct header function in QC combine_csvs.sh
• Correct qc pipeline field

v3.0.3

• Add pipeline to QC file
• Remove unnecessary local variables in qc_consensus.sh

v3.0.2

Remove unnecessary config check loop

v3.0.1

• Add git to environment.yml
• Correct join in Snakefile

v3.0.0

• Make environment.yml non-OS specific

• Record Git repo information in a yaml file in the processing directory

• Make the shiver mapper configurable in config.yaml

• Require the SMARTer adapter version (v2, v3) as input to setup.sh & prepare.sh and record in config.yaml

• Add SMARTer adapter trimming (3bp or 14bp, read 2), with the number of bps to trim determined by the SMARTer adapter version

• Rename rules and scripts to make it clear when trimming is being done

v2.0.0

• Move preprocessing before trimmomatic
• Refactor preprocessing script
• Adjust trimmomatic parameters
• Pass trimmomatic output to shiver
• Turn off trimmomatic in shiver
• Use bowtie2 as the mapper in shiver
• Use samples.txt in processing (rather than raw data) directory

v1.2.3

Simplify rule pipeline_trimmomatic params

v1.2.2

Update GitHub Actions

v1.2.1

• Add GitHub Action to lint with flake8
• Associated Python code updates

v1.2.0

Run pangolin update as part of pre-processing as it fails with qsub