Metator

- Add a prefix option for fasta files.

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

- Repair the pipeline module.

- 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.

- 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.

- Add iterative and cutsite alignment mode.