1.4

Hi, we're still here! 🐍 🐍 🐍

Major Changes:

• Every conda environement is now in a single singularity container. tools_paths.yaml file is now more slim.
• Module load environments are usually used on clusters. It's now possible, filling in the ENVMODULE key on tools_path.yaml file. 🤓

New features:

• Pilon was added as a new corrector using illumina reads
• Remapping of illumina reads over each obtained assembly is now possible using samtools flagstats.

Coding modifications:

• Pilon can be lauch recursively
• Report was updated to new tools

Documentation:

• Updating and improving documentation.

1.3.2

Minor Changes

Changing busco from conda to singularity
Separation of minimap and miniasm in 2 rules and integration of both in the time benchmark
Schema was modified to check conda paths

1.3.1

Minor Changes

• Fixing shasta option and singularity name
• Fixing bug with shub image on tools_path.yaml
• Fixing bug quast usage without reference

Documentation

• Update docs

1.3.0

IT'S CULEBRONT FIRST ANNIVERSARY !! happy birthday CulebrONT! 🎂 🐍 🤓

To celebrate this:

Major Changes:

• Fixstart is now launched at the end of the last step (assembly, polishing or correction) when activated by the user.
• Raven and shasta are now independant of Circlator.
• Minipolish is now independant of Racon.
• Some singularity containers are now conda environment.
• Update tools in containers.
• Simplification of config.yaml by splitting it in two files : tools and parameters.
• Improving the control of the user parameters using a new CulebrONT class. This class allow us to control better the modularity of CulebrONT.

New features:

• Parallelization of Medaka.

Coding modifications:

• Split Snakefile in several files by step.
• Rewrite report

Documentation:

• Update and improve the documentation.

1.2.0

A lot of thinks to list here :-D

• Assembled molecule is split before Nanopolish. Each segment is polished on parallel to improve speed and gain time. Segments polished are merged subsequently
• Fixstart step is now before to quality control but only if CIRCULAR is activated. rule run_fixstart is placed after of preparing_fasta_to_quality to make sure that all QC steps are performed on the 'fixed' molecules.
• Repertory architecture of CulebrONT output directory was modified
• The behavior of Quast and Mauve by using lambda wildcard instead of expand.
• We have included the possibility to specify optional parameters on configuration file to Flye and Medaka. Medaka options can be changed on feature, training and consensus steps.
• Medaka model are not available on CulebrONT repository anymore.
• Fixing bugs on mauve
• Documentation and report were upgraded

1.1.1

• fixing minor bugs on slurm_wrapper.py
• def get_threads on Snakemake was corrected to SGE or SLURM HPC

1.1.0

Three news assembles were integrated on culebrONT : Shasta, Smartdenovo and Raven 👍

• If circular is activated, assembly from these three new assemblers can be circularised by circlator.
• Singularity containers for these assemblers are available on singularity hub

Documentation is now on https://culebront-pipeline.readthedocs.io/en/latest/ 🥇

1.0.0

First release of CulebrONT pipeline.
CulebrONT is a snakemake pipeline to compare assemblies.
It inclues assembly, circularisation, polishing, correction and also check quality !
Developped to use with Oxford nanopore reads.
A very usefull report to help you taking decisions!