3.1.20220629

Minor updates relating to nextalign and nextclade updating to v2.1

• nextalign process command was updated
• nextclade process command was updated

Minor updates relating to fastp

• default fastp container was adjust to staphb

Updated corresponding datafiles

Updated version

Removed empty files

3.0.20220520

This is considered a major release because it has now been converted into dsl2, which is the current default for nextflow.

Other notable differences:

• freyja option paramaters have been added
• bamsnap and renaming of files have been dropped (filtering to a reference is still supported)
• containers now have versions on them
• bcftools variants is now true by default

2.4.20220407

This is a minor release.

• Pangolin V4 created some header parsing updates for the summary file, therefore, the summary file now includes additional pangolin columns
• freyja and multiqc have been added
• the config template has been adjusted to reflect the addition of new parameters
• images have been added to the readme

2.3.20220114

There are some major changes

• The default primer set is now artic's SARS-CoV-2 V4 primer set instead of V3
• The columns of the summary file are in a different order
  • but they now include pangolin's lineage calls
• The README has been updated to include information about minimum depth requirments
• New files in data to show change in columns for end user comparison

2.2.20211221

• Basically I put a script into a channel so that it would make it into docker containers on aws

What's Changed

• Erin dev by @erinyoung in #87

Full Changelog: 2.2.20211215.1...2.2.20211221

2.2.20211215.1

What's Changed

• Erin dev by @erinyoung in #86

Full Changelog: 2.2.20211215...2.2.20211215.1

2.2.20211210

• minor bug fixes that could've been avoided if I had developed tests beforehand

2.2.20211209.1

In this release:

• multifasta support
• under the hood, vadr, pangolin, and nextclade are not run individually any longer - this is due to adding in multifasta support
• nextclade prep process has been merged into the nextclade process - since nextclade is now only run once
• a new parameter designating with nextclade dataset to use is introduced params.nextclade_dataset = 'sars-cov-2'
• the algined fasta from nextclade can now be used to create a tree with iqtree
• set params.msa = 'nextclade' when params.relatedness = true
• a new script that uses pandas to combine nextclade, vadr, and pangolin results.
• This changes the columns of the summary file (sorry!) in a new process named combine_results
• using the quay.io/biocontainers/pandas:1.1.5 as the default container for the process summary and fasta_prep

2.2.20211209

In this release:

• multifasta support
• under the hood, vadr, pangolin, and nextclade are not run individually any longer - this is due to adding in multifasta support
• nextclade prep process has been merged into the nextclade process - since nextclade is now only run once
  • a new parameter designating with nextclade dataset to use is introduced params.nextclade_dataset = 'sars-cov-2'
• the algined fasta from nextclade can now be used to create a tree with iqtree
  • set params.msa = 'nextclade' when params.relatedness = true
• a new script that uses pandas to combine nextclade, vadr, and pangolin results.
  • This changes the columns of the summary file (sorry!) in a new process named combine_results
• using the quay.io/biocontainers/pandas:1.1.5 as the default container for the process summary and fasta_prep

2.1.20211120

Mostly minor fixes

• fixes samtools flagstats, coverage, stats, and depth issues when skipping trimming
• fixes summary file when importing fastas
• updated readme to include information about 'params.maxcpus' and 'params.medcpus'
• removes unneeded columns in summary file when starting from fastq files