Dev

See merge request genotoul-bioinfo/metagwgs!1

rename bin/Script_histogramme.R into bin/Script_hist_kaiju.R and modify it (issue length of match histogram resolved) #7, modify bin/Script_quantification_clusters_opti.py (variable names) #9, add option length name cd-hit (main.nf) #19, add subdirectories into results directory (main.nf) #20, modify process for creation database index kaiju(remove beforeScript) #7, add comments (main.nf), modify nextflow.config file

add script Script_renameVcn.py to rename contigs and genes in gff, faa and ffn files, add corresponding process in Nextflow pipeline (with modification of contigs and genes names in .fna file too) #14 and update of kaiju version for index but not tested #15

merge python scripts bin/Script_join_glob_clstr_contig.py and bin/Script_quantification_clusters.py and use of python template script #8 #9

add Python script Script_join_glob_clstr_contig.py to join tables with contig id, intermediate cluster id and intermediate cluster id, global cluster id, update Python script cd_hit_produce_table_clstr.py (add parenthesis when print is used), update nextflow.config file for standard profile only #8

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