v0.2.12

Fixed

• Medaka models added to container

v0.2.11

Changed

• --basecall_cfg is now used to determine suitable Medaka model, alternatively provide the name of a model with --medaka_consensus_model and --medaka_variant_model to override automatic selection.

v0.2.10

Fixed

• sample_sheet format in schema to expect a file

v0.2.9

Changed

• Updated description in manifest

v0.2.8

• Output QUAST stats for reference and denovo based assembly

v0.2.7

Changes

• Replace QUAST with MetaQUAST
• Add species ID to run summary table
• For reference based assembly --reference_based_assembly parameter should now be provided with a --reference. The default is to use denovo assembly.
• Tidy up presentation in report
• -profile conda is no longer supported, users should use -profile standard (Docker) or -profile singularity instead
• Docs update

Added

• nextflow run epi2me-labs/wf-human-variation --version will now print the workflow version number and exit

Fixes

• Prokka only runs in denovo assembly mode
• Tidy up report code

v0.2.6

Changes

• Added quast for assembly stats
• Remove sanitize option

Fixes

• Update syntax to fix reference error

v0.2.5

Changes

• Better help text on cli
• Fastqingress metadata map
• Use groovy script to ping after workflow has run

Fixes

• Output medaka vcf
• Remove reliance on simpleName

v0.2.4

Fixed

• Amend report name.

v0.2.3

Added

• Add read me docs.