2.2.0

CulebrONT release 2.2.0 🐍

New features :

• Medaka can now be run by segment or in oneshot way 👨‍🔧

Minor (but cool) changes 😎

• Smartdenovo and KAT use now only one thread by default

Fixing bugs 🐞

• Some logs were missing in several rules causing bugs

2.1.1

CulebrONT release 2.1.1 🐍

Minor changes

📁 restructuring the output file names and log files tree
🐛 fixing stdout error redirection for snakemake command
😄 fixing some bugs in report after renaming of files

Docs

🔢 some minor modifications in documentation

2.1.0

CulebrONT release 2.1.0 🐍

New features :

• Merqury was added as a new quality tool using illumina reads 👨‍🔧

Minor (but cool) changes 😎

• Tools in containers/Singularity.culebront_tools.def were upgraded
• Add nodelist in slurm profile

Fixing bugs 🐞

• Now CulebrONT checks if FIXSTART is activated while MAUVE and CIRCULAR are used
• Now CulebrONT checks reference when Assemblytics is used
• Now snakemake redirection stdout and stderr are correctly captured by culebront

2.0.1

CulebrONT release 2.0.1 🐍

We are (again) here !! because we love fix bugs 🐛 !

Minor (but cool) changes

🐞 now is possible to add nodelist slurm option in cluster_config.yaml. Cool to force a specific node of a partition.
📁 All assemblies for all samples can be found now in a single directory ASSEMBLIES

Fixing bugs

🐛 Fix bug in run_cluster command line. We have forgotten remove a parameter in a def and it broken all!!
🐛 Fix bug when singularity was used in cluster mode. Path problem of singularity image.

Docs

🔢 improving our english in docs (thanks @francoissabot @scunnac )

Minor changes for developers

🥇 improve test for gitlab and github

V2.0.0

CulebrONT release 2.0.0 is here !!! 🐍 🎉 🍺

🚀 This is a major release which break the compatibility with the code of the culebrONT 1.x versions

If a previous version was installed, please remove it after this new install ⚠️

New features 💄

📦 CulebrONT is now a python package, so install is easier by using pip3 install culebrONT
💡 CulebrONT uses click python library. It allows us high level command lines creation in this package !!!!

Major changes for the community ⚡

🚧 Reorder of full git repository in order to create PYPI package.
🎉 Easier installation, we improved local culebrONT install_local and HPC installation culebrONT install_cluster
🎨 More flexibility to change version of tools by using culebrONT edit_tools
🐛 Fix bugs in some rules which was still run when "false" value was filling in config.yaml file
🔒 Tools in containers/Singularity.culebront_tools.def were upgraded
🙈 Data test was upgraded

Major changes for developers 🔥

♻️ Code was reorder to bring a generic module snakemakeAsModule able to be reused in others snakemake projets.
🔧 Continuous integration of test by using tox and gitlab-ci

Documentation 📌

• Update install procedure for local and HPC
• Update running workflow on local and HPC
• Add culebrONT full commands avail on API section
• Add expert mode to more parameters' workflow (tools, ressources, ...)

1.7.0

CulebrONT v.1.7.0 🐍 :

⚠️ in this release you need to update your config.yaml file with the new considered arguments

Major Changes:

• Addition of a new 'MODE' parameter to FLYE and CANU: allows modification of the tool's basic option; for instance FLYE can use ''--nano-raw" if Guppy < v5 or "--nano-hq" if Guppy >= v5
• Fix bug "FLYE params not passed to Snakefile"
• Update tools versions in Containers/Singularity.culebront_tools.def
• local run now uses the true number of threads provided through -c option

Minor Changes:

• Raise an error on fastq files containing an underscore ("_") to warn of an error latter in the report
• Improved scripts for job submission

Documentation

• Update of documentation for installation
• Improving FAQ

1.6.0

CulebrONT v.1.6.0 🐍

Major Changes:

• A Docker virtual machine is now available to easy install CulebrONT in local mode. It contains all dependancies and tools used by CulebrONT! 🤓
• Upgrade submit_culebront.sh script to easier run culebront on local and HPC

Minor Changes:

• Fixing bugs to obtain dag and versions on report
• Reference file in data test was changed

Documentation

• Update documentation for easier installation using a new Docker virtual machine
• Update documentation with rules names
• Adding some FAQ

1.5.2

Minor Changes:

• Correction and cleaning of the code that permits to the versions of the tools to be printed nicely in the report.
• Correction of a bug of the dag graph in cluster mode
• Removing of the quality tool weesam

1.5.1

Minor Changes:

All tools versions now appear correctly in the report

1.5.0

CulebrONT v.1.5.0 🐍

Major Changes:

• CulebrONT class parse the use-envmodule and singularity arguments to check only the activated tools
• Adapt submit_culebront.sh script to profiles 🤓
• Envmodules and profiles are now available on gifts_files repertory
• Tools version are now in report 👍

Minor Changes:

• Fixing bug with hard path code on blobtools. Parameters nodes and names are given by user
• Fixing circular R script path
• Fixing hard path for busco
• Cleaning singularity Hub features because it is not maintained any more

Documentation

• Update documentation for easier installation using profiles on cluster
• Reorder documentation
• Adding some FAQ