This project is mirrored from https://*****:*****@github.com/EBI-Metagenomics/emg-viral-pipeline.
Pull mirroring updated .
- Aug 27, 2024
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Martin Beracochea authored
Update README.md
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- Aug 23, 2024
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Matthew DeMaere authored
Revised example commands to use $HOME rather /home/$USER, as the latter is not consistently valid across systems.
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- May 08, 2024
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Martin Beracochea authored
Merge small set of fixes for new release #123
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Martin Beracochea authored
I will update them after this release.
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Martin Beracochea authored
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Martin Beracochea authored
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Martin Beracochea authored
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Martin Beracochea authored
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Martin Beracochea authored
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- May 07, 2024
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Martin Beracochea authored
Prase.nf results are optional.
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- Apr 30, 2024
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Martin Beracochea authored
This is to prevent the pipeline from "failing" when there are no viral annotations.
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- Apr 25, 2024
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Varsha Kale authored
remove lsf requirement for ebi profile
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Varsha Kale authored
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- Oct 10, 2023
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Martin Beracochea authored
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Martin Beracochea authored
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Martin Beracochea authored
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- Sep 21, 2023
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Martin Beracochea authored
Fix Chromomap container
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- Sep 15, 2023
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Martin Hölzer authored
Fix the Chromomap container.
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- Sep 06, 2023
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Martin Beracochea authored
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- Jul 17, 2023
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Martin Beracochea authored
Adjustment of the voting scheme and updated viral taxonomy and bugfixes for new release
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Martin Beracochea authored
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Guillermo Rangel authored
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- Jul 14, 2023
- Jul 11, 2023
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Martin Beracochea authored
Metadata file v4, also included a warning about the deleted taxa.
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- Jul 05, 2023
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Martin Beracochea authored
Also removed duplicated file
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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) ... ```
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- Jun 30, 2023
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Guillermo Rangel authored
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- Jun 29, 2023
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Martin Beracochea authored
Adjustment of the voting scheme and updated viral taxonomy
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- Jun 28, 2023
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Martin Beracochea authored
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Martin Beracochea authored
And remove an unused python script
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Martin Beracochea authored
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Martin Beracochea authored
Created a references folder, we can keep small dbs or files in there. More portable. I've added a helper script to createa a ete3_ncbi lite sqlite db. Useful for testing.
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- May 30, 2023
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Martin Hölzer authored
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Guillermo Rangel authored
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- May 13, 2023
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Guillermo Rangel authored
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- Apr 28, 2023
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Martin Beracochea authored
Bugfix release - PR #94
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Martin Beracochea authored
Fasta IDs renaming fixed
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- Apr 27, 2023
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Martin Beracochea authored
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Martin Beracochea authored
Adjust the script to the new separator for the phage metatada on the fasta headers. From " " to "|"
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