3.7.20230523

• updates Freyja container

3.7.20230516

Minor Release:

• updates Freyja container
• updates nextclade/nextalign container

3.7.20230509

Minor Release

• updates Freyja container
• adds in missing mxp config files
• adds tests to GA (tests fail due to disk space and will need to be fixed for the next release)

3.7.20230502

In this release:

• updates Freyja container
• updates ivar version and adjusts the ivar module
  • fyi : the most recent update from ivar doesn't get incorporated into the multiqc report
• added size filter for ivar trim (size must be > 500)

3.6.20230425

Minor release:

• update readme
• update freyja container
• update nextclade dataset

3.6.20230418

Minor changes:

• adds ivar consensus version to summary file (#153)
• fixes how fastqc results are shown in summary file(#148)
• updates freyja and pangolin containers (#154 and #150)
• warns about using params.kraken2_organism (#152)
• Updates readme (#151 and #149)
• Adds artic 5.3.2 primer options (#146)
  • WARNING : untested feature as UPHL does not currently have files to test this with
• fixes how vadr results are shown in summary file (#148)

3.6.20230412

Minor release, BUT! there are changes to the summary file and a param has been removed. There are also changes to the config file template, as this is no longer called in the workflow.

Of note, the Github Actions (GA) to look for new container versions is working. This dramatically increases the amount of time needed to keep current as well as dramatically increases the notifications that this workflow receives.

Most notable changes are internal, so here's hoping nothing breaks for the end users.

In this version:

• All container designations have moved into each process in the module files
• UPHL ICA options have been added to each process in the modules files. These are commented out for the general user
• There are no more 'latest' container tags due to GA actions ability to notify of most relevant changes every Tuesday
• The results channels have been simplified to for_multiqc, for_summary, and for_version
• The summary file is created in a different way
• Fastas and multifastas can be read in via the sample sheet
• There is now ASCII art. You're welcome
• Updates to the readme
• Included Nextclade datasets for those who can't download it (set params.download_nextclade_dataset=false and predownloaded_nextclade_dataset=sars.zip)
• params.kraken2_organism has been removed. Percent human reads remains, but there is now a top hit and the percent by that top hit.

3.5.20230216

Minor release that fixes a major bug (unfortunately)

• Fixes typo in channel needed for relatedness
• Fixes bug in single end fastq files from SRA
• Adds in five more tests that things like this don't happen in the future

3.5.20230201

Minor release:

• updates a few containers
• adds sample sheet functionality
• add test profile
• organizes schema to alphabetical order

3.4.20221121

Minor Release:

• Adds primalseq primers