v0.9.9-gamma

Release based on the BCG branch. Changes include:

1. changes to the logic in identify_tophits_and_contaminants.py. Centered around identifying M. bovis based on the name "Mycobacterium tuberculosis variant bovis" leading to using tuberculosis as the reference.
2. As above, but adding logic to identify bovis based on its lineage (LA.1).
3. Changes to the pipeline so that every sample has allelic depth calculated
4. VCFMIX now runs on minos VCF, added in tweak to accept that style of VCF file
5. changes to containers to align with the above
6. Changes to workflow logic to correct bugs when running with a mixture of MTB and NTM samples
7. Update to parse_kraken_report.py to deal with some kraken hits having non-alphanumeric characters

What's Changed

• another change to containers by @WhalleyT in #94
• update config by @WhalleyT in #95
• Recursive decontamination by @WhalleyT in #96
• update tests by @WhalleyT in #98
• update final report to accept QC sucesses by @WhalleyT in #99
• Tbtamr by @WhalleyT in #100
• Collate by @WhalleyT in #101
• config by @WhalleyT in #102
• Empty vcfs by @WhalleyT in #106
• Ntmprofiler by @WhalleyT in #107

Full Changelog: v0.9.9-beta...v0.9.9-gamma

v0.9.9-beta

Added the following:

1. Multi-pass decontamination (two iterations)
2. Updated reporting to number passed on pass
3. "permissive" flag that allows samples failing decontamination to carry on
4. changed regex and arguments for python scripts to add in permissive flags and new names
5. containers updated (main issue being JRE in clockwork container)

Plus updates in v0.9.9-alpha

v0.9.9-alpha

Release preceding changes made in 0.9.9-beta, so TB-pipeline testing group have a fixed version to roll back to if required.

Includes:

• Changes to assembly_summary_refseq.txt
• switch from ftp to https
• addition of tmp dirs for tb-profiler
• thresholds for kraken report parsing (i.e. what is a contaminant)

v0.9.8

Updates include:

• Gnomonicus has been removed and replaced with TB-profiler
• Addition of climb config profile for running on the CLIMB-BIG-DATA Jupyter Notebook Server and k8s
• Minor updates to the reporting

v0.9.7

Updates include:

• Removal of the quality control step which stopped samples progressing further in the pipeline if the top hit from Kraken2 is not Mycobacteria or if there are less than 100k Mycobacteria reads. These samples that fail the Kraken2 QC step will now pass to Afanc for speciation, but will not progress further in the pipeline

• Updates to Afanc including the lineage designation work

The new release of the Afanc database is available at:
https://s3.climb.ac.uk/microbial-bioin-sp3/Mycobacteriaciae_DB_7.0.tar.gz

v0.9.6

Updates include:

• Afanc updated to v0.9.2-alpha
• Bug fix for VCFMIX
• Bug fix for software versioning parsing

A new release of the afanc database is available at:
https://s3.climb.ac.uk/microbial-bioin-sp3/Mycobacteriaciae_DB_6.0.tar.gz

v0.9.5

Release for UAT

Updates include:

• Afanc is now used for speciation and downstream reporting
• Mykrobe runs as an independent process
• Uses the new NCBI taxonomy for Mycobacteriaceae (Mycobacterium, Mycobacteroides, Mycolicibacter, Mycolicibacterium, and Mycolicibacillus)
• Gnomonicus and AMR catalogues have been updated
• Updates to the reporting

Bug fixes:
#15, #16, #18, #19, #20, #21, #22, #26, #27, #31, #32, #33

v0.9.4

Release Notes

Updates:

• Updated to gnomonicus 1.1.1 (with latest dependencies)
• Added flags for vcfmix and gnomon
• Updated stub-run and added CI for stub-run

v0.9.3

Release Notes

Updates:

• Added vcfpredict sub-workflow for VCFMIX and gnomon
• Added getversion sub-workflow for software versions json
• CI testing has been added for the python scripts

Bug fixes:
Fixes #4 and #11

v0.9.2

Release Notes

Updates:

• Mykrobe has been updated to v0.12.1
• Updates to the stability of the containers
• The perl scripts have been deleted and replaced with python scripts
• Tests have been added for the python scripts
• CI has been added for the container builds
• Config now pulls container images directly from quay.io (or uses cached images)

Bug fixes:
Fixes #6 and #9