3.13.20240319

Minor release with some construction "under the hood"

• updated pangolin to 4.3.1-pdata-1.26
• updated freyja to 1.4.9-03_18_2024-00-45-2024-03-19
• moved aci to staphb/aci:1.4.20240116
• lists all versions for all processes
  • includes software versions in multiqc
• compresses classified and unclassified kraken2 reads in fastq.gz files (instead of fastq)
• run report files have been renamed to start with "cecret"
• allows multiple sequence alignment file from nextclade to be used with iqtree2 for phylogenetic tree creation

"Under the hood" changes

• adds GA for kraken2
• adds task.ext.prefix, etc for each process (still needs the meta.id)

3.12.20240312

Minor release:

• updates Freyja to 1.4.9-03_12_2024-00-43-2024-03-12
• updates nextclade to 3.3.1

3.12.20240227

Minor release with mainly version bumps:

• FEATURE : now publishes Kraken2 unclassified files
• updated nextclade to 3.0.3
• updated freyja to 1.4.9-03_04_2024-00-46-2024-03-05
• moved heatcluster, multiqc, and freyja to staphb's containers

3.12.20240221

• adds bbnorm option (set params.bbnorm = true as false is the default)
• updates freyja to 1.4.9-2024-02-20
• updates nextclade to 3.2.1
• updates included SARS-CoV-2 nextclade dataset (use by setting params.download_nextclade_dataset = false)
• adds fixed file for pango-collapse
• updates pangolin to 4.3.1-pdata-1.25.1
• sets ACI and IGV-reports to false by default

Notes : |
SARS-CoV-2 sequencing is changing. Locally, we are seeing fewer samples per run which is increasing the number of reads per sample in ways that lengthen the time of this workflow unnecessarily. We are still looking at different normalization options, but if others are seeing the same issues we are, there's a new option to use bbnorm to normalize reads to 200X coverage. This is currently set to false as default until more testing is done, but can be used by setting params.bbnorm = true. This does not seem to impact the desired results, but does cut runtime down significantly. (see #298 for more information.)

Outside of the core workflow, ACI and IGV-reports processes take a long time to run. For many users that are not manually inspecting variants or testing out new amplicon schemas, these tools are not needed or wanted. They haven't been removed, they've just been turned off by default. To have them run set param.aci = true for ACI and param.igv_reports = true for igv-reports.

3.11.20240213

• updates freyja to 1.4.9-2024-02-13
• updates nextclade to 3.2.0

3.11.20240206

Minor release:

• Updates Freyja to 1.4.8-2024-02-06
• Updates IQTREE2 to 2.2.2.7
• Updates NextClade to 3.1.0
• Updates PhyTreeviz to 0.2.0

3.11.20240130

Minor update:

• update included SARS-CoV-2 nextclade dataset (use by setting params.download_nextclade_dataset = false)
• update nextclade to 3.0.1
• update freyja to 1.4.8-2024-01-30

3.11.20240123

Minor update

• updates Freyja to 1.4.8-2024-01-23
• updates pangolin to 4.3.1-pdata-1.24

3.11.20240116

Moderate update:

• update nextclade to version 3.0.0
  • remove nextalign multiple sequence alignment option - well, replaced it with nextclade, but all nodes are included
• update included SARS-CoV-2 nextclade dataset (use by setting params.download_nextclade_dataset = false)
• separate aci to run per sample instead of per run
• update samtools and bcftools to 1.19
• update aci to 1.4.20240116
• update freyja to 1.4.8-2024-01-16
• update vadr to 1.6.3

3.10.20240109

Minor Release:

• Updates Heatcluster to 1.0.2c
• Updates Freyja to 1.4.8-2024-01-09