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This project is mirrored from https://*****:*****@github.com/EBI-Metagenomics/emg-viral-pipeline. Pull mirroring updated .
  1. Aug 27, 2024
  2. Aug 23, 2024
    • Matthew DeMaere's avatar
      Update README.md · cd3133dd
      Matthew DeMaere authored
      Revised example commands to use $HOME rather /home/$USER, as the latter is not consistently valid across systems.
      cd3133dd
  3. May 08, 2024
  4. May 07, 2024
  5. Apr 30, 2024
  6. Apr 25, 2024
  7. Oct 10, 2023
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  10. Sep 06, 2023
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  13. Jul 11, 2023
  14. Jul 05, 2023
    • Martin Beracochea's avatar
      Updated metadata file and warning message. · 88b26f92
      Martin Beracochea authored
      Also removed duplicated file
      88b26f92
    • Martin Beracochea's avatar
      Metadata file v4, also included a warning about the deleted taxa. · 2ca3f64a
      Martin Beracochea authored
      The warning message looks like:
      ```
      nextflow run virify.nf --meta_version v4 --fasta nextflow/test/assembly.fasta
      N E X T F L O W  ~  version 23.04.0
      Launching `virify.nf` [sharp_carlsson] DSL2 - revision: 690a9ff68f
      
      Profile: standard
      
      Current User: mbc
      Nextflow-version: 23.04.0
      Starting time: 01-04-2023 21:09 UTC
      Workdir location:
        /home/mbc/projects/emg-viral-pipeline/work
      Databases location:
        nextflow-autodownload-databases
      
      CPUs to use: 2
      Output dir name: results
      
      Dev ViPhOG database: v3
      Dev Meta database: v4
      
      Only run annotation: false
      
      Warning: --meta_version v4 does not include the following discontinued virus taxa
      (according to ICTV) anymore and they have been excluded from the dataset.
      
      Siphoviridae
      Podoviridae
      Myoviridae
      Caudovirales
      Allolevivirus
      Autographivirinae
      Buttersvirus
      Chungbukvirus
      Incheonvirus
      Leviviridae
      Levivirus
      Mandarivirus
      Pbi1virus
      Phicbkvirus
      Radnorvirus
      Sitaravirus
      Vidavervirus
      
      executor >  local (6)
      ...
      ```
      2ca3f64a
  15. Jun 30, 2023
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  21. Apr 27, 2023