v0.4.5

What's Changed

• Make using sample ID as locustag optional. Fixes issue where long sample IDs caused pipeline failure. (Issue #39)
• Fixed publishing prokka outputs (Issue #49)
• Removed --versioned_outdir param (Issue #50)

Full Changelog: v0.4.4...v0.4.5

v0.4.4

• Further changes to address low-coverage samples when annotation with prokka or bakta is performed (Issue #36)

v0.4.3

• Handle low-coverage samples, which produce empty assemblies (Issue #36)

v0.4.2

• Fixed issue where sample IDs were determined incorrectly for long reads in hybrid assemblies (Issue #34)

v0.4.1

• Updated bakta to v1.5.1
• Write tmp files to process work directory instead of /tmp in bakta process (Issue #32)

v0.4.0

• Use unicycler for all assemblies (Issue #29)
• Make gene annotation optional. Either prokka or bakta (or both) can be run with the --prokka or --bakta flags.

v0.3.0

• Added long-read-only assembly mode with Dragonflye (Issue #21)
• Fixed issue where --samplesheet_input was incompatible with --hybrid mode (Issue #27)
• Updated provenance format (see README)

v0.2.2

Features

• Added process_name field to provenance entries (Issue #17)
• Added --versioned_outdir flag for storing outputs in versioned sub-directory (Issue #18)

v0.2.1

Fixes

• Tag output filenames with name of assembler that was used, to guarantee unique output filenames when samples are re-analyzed (Issue #13)
• Replace json-formatted parsed quast output with a csv output with cleaned headers (Issue #14)

v0.2.0

Features

• Support 'SampleSheet' input mode (Issue #7)
• Collect provenance information for each sample (Issue #6)
• Add read length-related fields to fastp.csv output (Issue #9)