Release v1.3.2

What's Changed

• Add catch for no reads being left after fastp filtering by @BioWilko in #74

Full Changelog: 1.3.1...1.3.2

Release v1.3.1

What's Changed

• Main unstable by @rmcolq in #72

Full Changelog: 1.3.0...1.3.1

Release v1.3.0

• Refactor code around extracting read fractions and reads by taxa. This included removing support to extract sub-species and sub-sub-species reads to files because kraken assignments aren't confident enough to justify it. Also resolved a bug where the read counts in the summary file were on occasion double counted.
• Add kraken_confidence parameter
• Make alignment use short-read preset when we have illumina data
• Catch where out_dir or output used on command line instead of outdir
• Run extract steps with progressive memory allowed so that fewer resources required more often

What's Changed

• Paired run by @rmcolq in #66
• Fix missing read file 2 by @rmcolq in #70
• Dev refactor kraken by @rmcolq in #71
• Updated short read handling by @rmcolq in #68

Full Changelog: 1.2.1...1.3.0

Release v1.2.1

What's Changed

• Fix missing read file 2 by @rmcolq in #67

Full Changelog: 1.2.0...1.2.1

Release v1.2.0

What's Changed

• Sync unstable with main by @rmcolq in #51
• Small fixes by @rmcolq in #52
• add centrifuge module by @rmcolq in #54
• change publish path by @rmcolq in #55
• update kraken resources by @rmcolq in #56
• Merge in main_unstable by @rmcolq in #58
• convert warning file to json by @rmcolq in #63
• Remove spike ins by @rmcolq in #62
• add taxid and taxon human readable name to the spike refs, and pass t… by @rmcolq in #65
• Integrate spike handling to main by @rmcolq in #64

Full Changelog: 1.1.3...1.2.0

Release v1.1.3

Dump workflow version to new output file pipeline_info/workflow_version_{unique_id}.txt

Full Changelog: 1.1.2...1.1.3

Release v1.1.2

Changes include:

• Bump to newest version of kraken2-server in response to bug fix

What's Changed

• bump version of... by @rmcolq in #50

Full Changelog: 1.1.1...1.1.2

Release v1.1.1

Changes include:

• Fixed a minor bug #47 which occurred when taxonomy database was out of sync with the kraken database

What's Changed

• force kraken... by @rmcolq in #48

Full Changelog: 1.1.0...1.1.1

Release v1.1.0

Small changes to output file formats including some renaming and the addition of a dedicated viral read fraction output.

Changes include:

• Added viral read fraction output
• Minor formatting updates, specifically improving consistency to the usage of double quotes instead of single quotes
• Docker container version updates
• Updates to conda profile versions and dependencies

What's Changed

• Add viral by @rmcolq in #46

Full Changelog: 1.0.0...1.1.0

Release scylla v1.0.0

First full release