VERSION 1.1.3 "Cascade" - 23th february 2021

Added

• "spygen origine" format (one single .dat file for one single .fastq file) can be processed
• UNIT TEST 01_settings/readwrite_rapidrun_demultiplexing.py barcode_tags_duplicated.csv has exactly 2 columns (original, duplicated)
• TEST dataset to check in few seconds if the whole workflow works fine on RAPIDRUN case
• TEST dataset to check in few seconds if the whole workflow works fine on CLASSIC case
• copy and rename files generated from 19_otu_table and 24_table_assigned_sequences to results folder
• resources job: number of parallelized jobs are limited by the resource "job"
• scripts/prepare_spygen_data.py generates the all_samples.csv file from SPYGEN "standard" information file and {marker}.dat files
• TEST integrity of .dat files

Changed

• all worklows are merged into a single one
• results subfolders are generated automatically
• unique scripts, rules and envs folders
• Demultiplex: no_indel option cutadapt to prevent insertion between tags and primers
• Alternative workflow to perform taxonomic assignment wihtout ecotag
• Fix wildcards in CLASSIC mode
• convert scripts/scripts/OTU_contingency_table.py code from python2 into python3
• update cutadapt version 2 to cutadapt version 3.2
• Fix SettingWithCopyWarning pandas dataframe
• factorisation folder results generation
• Fix data export

Removed

• old folders and scripts 01_settings, 02_assembly, 03_demultiplex, etc...
• old preexisting subfolders into results folder
• clean.sh script which is now useless
• rename.sh script which is replaced by a rule in Snakefile