Tags give the ability to mark specific points in history as being important
  • 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
  • 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
  • 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
  • V1.1
    - Add taxonomic affiliation of contigs
    - Add Singularity container
    - Setting up configuration files
    - First optimization of memory and CPU
  • V1.0
    First release.