Version 0.10.0

• Bug fixes when downloading reads from the ENA.
• Use Minos version 0.12.0
• When downloading data for remove contamination, NTM reads are now classified as contamination (previously, the reads would be kept and the number of them reported)

Version 0.9.0

Added option --gvcf tp variant call pipeline, to make a gVCF file

Version 0.8.3

• Add option to change bwa threads in remove contamination pipeline
• Use minos 0.10.0, which does homozygous genotyping

Version 0.8.2

Adds contig header lines to final.vcf file made by variant calling pipeline.

Version 0.8.1

Update to use latest versions of mykrobe, gramtools, and minos

Version 0.8.0

• clockwork script now logs to stdout (issue #57)
• python code reformatted with Black
• update to latest mykrobe (mykrobe commit b47f6241cfb2d223bb53aafd90a3f91d97248052)

Version 0.7.8

• fixes issues with downloading genomes from HMP
• genomes are not downloaded during container build. Instead, script to download them can be run using the container.

Version 0.7.7

Upgrade to minos version 0.9.1 to fix a bug introduced in previous commit

Version 0.7.6

Upgrade to minos v0.9.0, which has a bug fix for some legacy code which breaks when jobs crash and get resumed by nextflow.

Version 0.7.5

Upgrade minos to 0.7.0 so multisample pipeline parallelises build of chunks using nextflow