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
andenvs
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