v2.2.1

• bump pysam min pin to >=0.20.0
• bump samtools min pin >=1.16.1

v2.2.0

• update viral-baseimage to 2.2.0, bearing underlying OS upgrade from Ubuntu 18.04 LTS (bionic) to Ubuntu 22.04 LTS (jammy)
• build fixes for documentation (dependency changes) to fix local builds and builds on ReadTheDocs
• migration from Travis CI to GitHub Actions for testing and docker image deployment to quay.io

v2.1.33

• push R fix into docker image [#77]
• add median and mean options to binning stat for plot_coverage [#76]

v2.1.32

Update picard 2.25.5 -> 2.25.6 (#75)

v2.1.31

• update picard 2.25.4 -> 2.25.5 to address intermittent NullPointerException when demultiplexing NovaSeq runs

v2.1.30

illumina_demux changes:

• remove deprecated max_reads_in_ram_per_tile from picard opts
• expose picard opt sort (boolean for sorting reads, or not sorting them)
• also re-enable Intel compression rather than JDK deflater

v2.1.29

• upgrade picard 2.24.0 -> 2.25.4 which fixes bugs in picard 2.25.[0123] related to demultiplexing NextSeq 2000 and NovaSeq 6000 runs

v2.1.28

Correction to value for sequencer_model in runinfo json output

v2.1.27

illumina_demux: coerce all json metadata output values to strings, to facilitate their use in WDL

v2.1.26

• illumina.py flowcell_metadata now returns UNKNOWN rather than an error if it cannot figure out the model of sequencer from the flowcell ID or tile count