Version 1.3.0

Version 1.3.0 - 2023-11-09

• Merge MetaVIR (https://github.com/ABignaud/MetaVir) module to MetaTOR.
• Automatic generation of the compressed and sorted pairs files in the main
  pipeline.
• Correct QC issues with low-quality libraries.
• Add a conda environment file.

Version 1.2.8

Version 1.2.8 - 2023-04-12

• Correct issue with anvio binning file.

Version 1.2.7

Version 1.2.7 - 2023-04-07

• Correct bug during final plot generation.

Version 1.2.6

Version 1.2.6 - 2023-04-05

• Correct bug of contigs data final bin value from multiple recursive steps.

Version 1.2.5

Version 1.2.5 - 2023-04-05

• Remove recursive parallel which seems to failed in some case.
• Correct bug of contigs data final bin value from multiple recursive steps.
• Add exception to avoid error while mutliple metator are started from the same
  working directory.

Version 1.2.4

Version 1.2.4 - 2023-04-04

• Add a prefix option for fasta files.

Version 1.2.3

Version 1.2.3 - 2023-04-03

• Modify pairs option as an argument for QC module.
• Correct bug if only one MAG corrected in the recursive step.
• figures to work with miComplete
• Improve quality check metrics based on mock community results.
• Update QC tests.

Version 1.2.2

Version 1.2.2 - 2023-03-29

• Repair the pipeline module.

Version 1.2.1

Version 1.2.1 - 2023-03-29

• Make scaffolding optional in pipeline.
• Remove the option to start with network file.
• Allow parallel scaffolding at the end of the pipeline.
• Force pairix index used in the contact map module.
• Change pairs from option to arguments to handle easier multiple files as
  arguments.
• Debug scaffold module default parameters.
• Update docs.

Version 1.2.0

Version 1.2.0 2023-03-17

• Remove the skip validation option.
• Use miComplete instead of checkM for the recursive step.
• Make multiple recursive step if necessary.
• Sort pairs and do the scaffolding in the pipeline module.
• Add QC, pairs and scaffold modules.
• Correct pairs indexed loading.
• Add option to remove reads mapping at the edges of the contigs.
• Add possibility to used compressed pairs as input.
• Parallelization of the recursive step.
• Change bin id to make them sortable.
• Correct reads extraction bugs for contact map module.
• Correct bugs from cutsite mapping mode.
• Remove Looseversion sorting Warning.
• Update requirements file.
• Change output plot colors.
• Add tests for QC module.
• Update tests of network, partition and validation modules.
• Update documentation.