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