Version 0.7.4

Clockwork was unaware of the latest built-in panel for Mykrobe (201901). Fixed.

Version 0.7.3

Fix install script so it uses pip3 for Mykrobe

Version 0.7.2

Update version of minos (0.6.0)
Update mykrobe
Add indexing of sorted bam, which allows multi-sample pipeline to just use exactly the reads we need (not using unmapped any more)

Version 0.7.1

Update to minos 0.5.1

Version 0.7.0

• Use ubuntu 18.04 (which is LTS) instead of 17.10
• option to skip remove contamination pipeline (by running "fake" remove contam pipeline)
• Use latest gramtools and minos (0.5.0)

Version 0.5.2

• gramtools update c80672642d05f2f333b0c5fcdf9025a0ceac7905
• minos update 0.4.1

Version 0.5.1

• Add mykrobe pipeline
• Prevent remove contam pipeline from being run more than once on any sequence replicate
• Add task find_data, to report metadata from DB and location of files on disk
• Update gramtools and minos to latest versions

Version 0.4.0

• base VM now Ubuntu 17.10
• update minos to 0.4.0
• added simple merging of VCF files
• truth_ref option added to variant call pipeline
• make kmer counts file from cortex binary, during variant call pipeline
• new task minos_make_multi_sample_input to make input data to minos pipeline multi_sample_pipeline

Version 0.1.7

Two small bug fixes:

1. Error (chdir) when running spreadsheet validator

2. Repair genome BCSX00000000 after downloading, which had every contig twice.

Version 0.1.6

• new sequencing instruments added to allowed ENA list
• option to keep BAM file in variant call pipeline