optimization code Script_quantification_clusters(_opti).py add process generating correspondence table between individual clusters and contigs add process (to improve) generating merge of correspondances tables individual clusters - contigs and global clusters - individual clusters update process calculating read counts for each global cluster (generation of file containing name of count files and use of optimized script Script_quantification_clusters_opti.py instead of Script_quantification_clusters.py) #8 #9

Remove script bin/new_script.py which is renamed and update in bin/Script_quantification_clusters.py #9

update Script_quantification_clusters.py with english comments and variable names and deletion of useless script lines #9

modif main.nf to change script name for quantification_table process and modif name new_script.py (Script_quantification_clusters.py) and add comments #9

modif Scripthistogramme.R add new_script.py quantification summary (replace script_synthesis_quantifications.py) update main.nf and nextflow.config #9

add process to generate summary table with reads quantification for each cluster and each condition add python script in bin folder update of nextflow.config file #9

add process with python script cd_hit_produce_table_clstr.py and update kaiju process with for loop and script R Script_histogramme.R add bin folder with these two scripts and update of config file #6 #7

add kaijudb add kaiju and kronas after kaiju add assembly with megahit or mataspades add prokka add individual cd-hit add global cd-hit #6 #7

add sickle optional add new names channels and process add profile configuration file add modules slurm #1

add .gz out files cutadapt and sickle add cutadapt options add parameters in helpMessage add fastQC add multiQC add config file local #1