v2

There are multiple fixes and some new features in this version.

Utilities:

• INSTALLATION. Pling is finally installable, making it easier to run. Conda install is now also available
• Updated documentation

New features:

• Skip integerisation and use your own custom integer sequences instead - #63
• Can now run on linear genomes and regions of genomes - #44 and #6
• Optionally output Cytoscape formatted json files of network visualisations - these can be loaded directly into Cytoscape

For details on any of these please see the documentation.

Bug fixes:

• Fix #71
• Fix #57 - this fix in certain cases changes the integerisation, and the DCJ-Indel distances, but only in already quite diverged plasmid with previously high DCJ-Indel distances. Therefore this fix is unlikely to affect any clustering results. Please see the issue for a more detailed discussion.
• MAJOR fix: we have been using DCJ-Indel distances as weights in our clustering algorithm, without realising that the algorithm treats more weight as more favourable, i.e. edges with larger DCJ-Indel distances are more favourable. This is conceptually completely incorrect, and the opposite of what we would want. We have updated our plasmid network package plasnet to use the unweighted version of asynchronous label propagation. Version 0.6.0 of plasnet will be enforced as the minimal version required for pling. This change has not affected any of the smaller datasets we have previously run on (including our paper results), but does appear to affect the clustering for larger datasets (order of a 1000 and up)

v1.1.1

• Switched to more recent version of bakta (v1.9.3)
• Run panaroo with --remove-invalid-genes flag to ensure it can always handle bakta output
• Removed defaults channel from conda environment configuration files, as anaconda can no longer be used by orgnaisations with >200 people

v1.1

• No longer error out in file concatenation steps
• Improved memory use in initial batching step
• If performing sourmash prefiltering, rejected pairs of plasmids and their sourmash continament distance are now stored in not_pairs_continament_distance.tsv
• Updated documentation

v1.0.3

Fixes bug where singularity was still being used in gen_minimap_input rule in annotation workflow

v1.0.2

Fixes minor key error bug in integerisation from annotation workflow

v1.0.1

Some minor bug fixes and other misc smaller changes:

• Fixed a bug where the config file being generated by run_pling.py was in a format that sometimes got misread by Snakemake (adding excess whitespace)
• Fixed bug where integerisation would error out after 8 iterations of overlap fixing when there were only two matches between a pair of plasmids -- set a new breakoff point for number of iterations exception
• Added warning messages when overlap fixing gets broken off prematurely due to exceptions

v1.0

First release, should be reasonably stable.