# v2.4.3
*Eggnog mapper execution speed improved
*Replacement of cd-hit-est by cd-hit (faster) and correction of a bug in proteins predicted by prodigal
*Improved documentation (gitlab pages)
For details you can see:
https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/milestones/9#tab-issues

 # v2.4.2
 Release: metagWGS v 2.4.2
Fix bug in binette and others

 # v2.4.1

 # v2.4

 Release: v2.4
 For details you can see: 
https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/milestones/8#tab-issues

 # V3.2.1

 Release: V3.2.1
* Fix remaining conflicts from last realease
* Update documentation
* Fix sample name in taxonomic affiliation plots
* Update multiqc config #210
* Add header to metaWRAP scripts

 # v2.3
For details you can see: 
https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/milestones/7#tab-issues

 # V2.2

 Release: V2.2
DSL2 version

- pass to DSL2 to get 2 workflow (Short-read and HiFi)
- gene are named with feature (prot/rrna)
- aln2taxaffi.py refactored to use new_taxdump and prot.accession2taxid.FULL
- add header in diamond output and use it while parsing
- replace mosdepth by samtools coverage
- replace bedtools bamtofastq by samtools fastq
- check gff valididy after prokka
- simplify config files
- update documentation
- chunk assembly to reduce process time of filtering step
For details you can see: 
https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/milestones/5#tab-issues

 # V2.1

 Release: V2.1
- Multiple refactoring actions on metagwgs main script
- Rename some output files and reorganize output directories: i.e: assembly step
- Add mosdepth for contigs depth count + add mosdepth singularity image recipe
- Add taxonomy_dir parameter to use already downloaded taxonomy database
- Add functional tests script to test the pipeline output on reviewed results after functional modifications + add README
- Update documentation for metagwgs
- Change config for test_genotoul_workq parameters
- Change metaspades and megahit to unique assembly process
For details you can see: 
https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/milestones/6#tab-issues

# V2.0

- Add CI/CD
- Add direct download of Singularity containers
- Add deduplication of reads
- Add filtering of contigs
- Add functional annotation of genes + associated Singularity container
- Add quantification of reads by functional annotation
- Add first strategy of binning (adapted from nf-core/mag v1.0.0)
- Add first strategy of taxonomic affiliation of bins (from nf-core/mag v1.0.0)
- Add summary tables for taxonomic affiliation of contigs
- Add modularity of the pipeline: --step parameter
- Add documentation
- Improvement of MultiQC report: add modules into MultiQC and use of them into metagWGS
- Improve README
- Setting up configuration files
- First optimization of memory and CPU for test data
For details you cas see: 
https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/milestones/3#tab-issues

 # V1.1

- Add taxonomic affiliation of contigs
- Add Singularity container
- Setting up configuration files
- First optimization of memory and CPU
For details you can see: 
https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/milestones/2#tab-issues

 # V1.0

First release.
For details you can see:
https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/milestones/1#tab-issues