Release v0.0.9

What's Changed

Documentation

• Added information on the associated prublication & the reproducibility information related to it.
• Update copyright years.

Bugfixes

• Fixed code echo in variantreport (changes)
• Fixed incorrect use of na_if (changes)
• Fixed limitations to the size of column names in certain cases (changes)
• Fixed deconvolution for samples with no distinguishable variants (changes)

Full changelog and commit overview: v0.0.8 -> v0.0.9

Release v0.0.8

What's Changed

• Database downloads are now integrated into the pipeline.
• Added three more deconvolution methods and made weighting by mutation coverage optional.
• Added several options to use different starting files besides FASTQ reads.
• Added several options to let the pipeline stop after generating certain files.
• Made run parameters extensively customizable.
• Minor changes to report layout and formatting.
• Major code refactoring.
• Minor changes to report layout and formatting.
• Minor changes to output files and their locations.

Full changelog and commit overview: v0.0.7 -> v0.0.8

Release v0.0.7

What's Changed

• Deconvolution Improvements by @vfschumann in #115

Full Changelog: v0.0.6...v0.0.7

Release 0.0.6

This release adds support for single-end samples to the pipeline and the main report received some polishing.

What's Changed

• Rename by @rekado in #106
• enable single end input by @alexg9010 and @vfschumann in #100

Full Changelog: v0.0.5...v0.0.6

Release 0.0.5

This release includes files missing from the previous release and adds sample data and tests.

Release 0.0.4

release version 0.0.4 (pre-print version)

Version 0.0.3

This release includes a number of minor bug fixes, as well as an update to the runner script.

Version 0.0.2

This release includes files that were missing in 0.0.1.

First Release

This is the first release of the PiGx SARS-CoV-2 wastewater sequencing pipeline.