short-read-mngs-v6.1.5

Optimize idseq-dedup cluster file parsing.

short-read-mngs-v6.1.1

Bug fix: wrong lengths for the NT part of merged counts.

short-read-mngs-v6.1.0

• Adds new step for computing a single classification based on both NT and NR results for both per read taxon counts and contig statistics
• Simplifies CombineTaxonCounts to enable using it for combining the extra taxon counts
• Adjust average alignment length to use one nucleotide as reference (for merged NT NR only)
• Bug fix: Taxon blacklist was not having any effect since we were reading from additional_attributes instead of additional_files.

short-read-mngs-v6.0.1

Fix bug with reading header of idseq dedup cluster file

short-read-mngs-v6.0.0

replace cdhit-dup with idseq-dedup

consensus-genome-v1.4.0

• Add samtools_depth.txt file to the Consensus Genome output download ZIPs.

consensus-genome-v1.3.0

• Add support for single-end fastqs
• Bug fix: non compressed input fastqs would generate wrong number of total reads
• Improve lack of reads detection on filter reads

Ensure latest release has all changes

This release is to fix some versioning issues we've had recently. It adds no changes it just ensures the latest release has all of the changes.

short-read-mngs-v5.0.0

Complete switchover from idseq-dag to idseq-workflows and upgrade to a new versioning system. Moving forward, new workflow versions will be documented here as Github releases. Release notes for versions prior to v5 are documented in the idseq-dag README: https://github.com/chanzuckerberg/idseq-workflows/tree/main/short-read-mngs/idseq-dag#release-notes.