v1.0.0

New features

• CLI wrapper to call zAMP modules

Updates

• Updated modules for database training, in-silico validation and main taxonomic classification
• Updated tools to latest versions, including assembly_finder
• Database support for SILVA138.1, greengenes2 and UNITE

What's Changed

• Add cli wrapper and species names collapsing by @farchaab in #47
• Add working run command by @farchaab in #48
• PR to fix krona plots by @daulet-a in #51
• merge in-silico module branches by @farchaab in #52
• updating in silico module by @vicasze in #49
• Updated SRA download by @farchaab in #53
• Bioconda recipe by @vicasze in #54

New Contributors

• @daulet-a made their first contribution in #51
• @vicasze made their first contribution in #49

Full Changelog: v0.9.20...v1.0.0

v.0.9.19

Summary

Release to update tools and work with latest snakemake and apptainer

Details

Changes

• ef2d166 Update the pipeline to the latest Snakemake version (8.10.6)
• bf0ca40 Update multiQC and cutadapt
• afa1f5d Update DADA2, fastQC, picrust2
• 3d8ea94 Add the Family id during database prep in case multiple gens were remplaced by a spaceholder

Fixes

• 1bbda71 Fix deprecated Bio.Alphabet
• 083b163 Fixed workflow attribute error for singularity
• df44385 aec472c 1ce5a4d Fixed SRA
• a13174b Fixed decipher path

Pull requests

• Sedreh by @Sedreh in #33
• Update make_input_lists.py by @Sedreh in #34
• Update KRONA_plots.R by @Sedreh in #35
• Update under_the_hood.rst by @valscherz in #37
• Release 0.9.19 by @farchaab in #40
• Fix formatting and NameError by @farchaab in #45

New Contributors

• @Sedreh made their first contribution in #33
• @farchaab made their first contribution in #40

Full Changelog: v.0.9.18...v.0.9.19

Minor fixes

Minor fixes added since last release:

• MultiQC is again functionnal for execution after error filtration in DADA2 (5f62464)
• TreeShrink was added to identify potentially spurious ASV (683ea88)
• Trimming of primers in insilico was unified with main pipeline to be able to generate the exact same sequences (b19db24)
• a script was added to re-orientate amplicons after insilico extraction (6eb7625)
• functionnality of Qiime2-based insilico control was restored (9dbead4, d97f8a3)
• Fixed a miss-alignement in vsearch command that caused errors (d4141f8)

January 2021

Many small fixes:

• FastQC output is now temp
• clean-up of in-silico code
• added compatibility with single-end reads
• start to work on documentation
• cutadapt is now used to extract amplicon regions in ref database preprocessing
• fixed missing font for DADA2 graphs
• logs are simplified (tool logs are not recorded in dates directories anymore. Only execution logs are).
• ...
  Next steps:
• continue doc
• complete R shiny to QC results

Single-end compability

Add compatibility with single-end reads

Restructured pipeline

This release if the first since complete restructuring of the pipeline:

• A Singularity container is now defined for each rule, instead of having a big and hard to maintain container as previously.
• Pipeline preprocessing and formatting for the different classifiers is now in a dedicated worfklow.
• Original RDP is now implemented, with pretraining of the classifier during DBprocessing and optional rules to validate its performance.
• Reference databases were removed of this git repository (were too big). Their location (path) and name (directory at this path) must now be defined in config.
• Cutadapt settings were changed to filter out sequences without a primer at the expected position. This was implemented to avoid the inclusion of sequences in the wrong direction which would mess with phylogeny.

Traceability is now improved by :

• The recovery of the current commit and user in logs, including for DB processing.
• Hash generated during DB processing

Future improvements:

• Check for reference DB hash before tax assignment.
• Set the Shinyapp in a container.
• Generate a report to QC the whole process.
• Document with Read the Doc.
• Implement Travis to validate releases.

Minor corrections

Since last update:

• Correctred CLR transformation (#21)
• Update cutadapt to version 2.10. Now filters out raw reads without primers to discard sequences in the wrong direction. (#22)

Simplified pipeline

Since last release, we:

• Simplified the output (and the config file) by removing figures (barplots, heatmaps etc...)
• Updated to Qiime2 2020.02
• Updated to picrust2 2.3.0

Minor updates

Since v.0.9.11:

• force interactive plots for MultiQC of individual run
• update threads management for vsearch and DADA2
• Minor code clean-up
• Revised list of phyloseq output (breaks config file)

Minor update

• Pipeline was still having error with certain normalization methods and "-" in samples names
• Assembly finder environment was not pre-build in conda