EBI-Metagenomics/emg-viral-pipeline

📋 Changes

• [nf-schema](https://github.com/nextflow-io/nf-schema) plugin was missing from the pipeline dependencies, which broke the pipeline if the plugin was missing from the env.

📋 What's Changed

• Support compressed fasta and user proteins by @mberacochea in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/165
• Do not consider fraggenescan proteins in the annotation module by @mberacochea in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/166
• Bugfix/write gff missing contigs when user provided proteins by @mberacochea in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/167
• Feature/user proteins filter out proteins not in contigs by @mberacochea in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/168
• Full Changelog: https://github.com/EBI-Metagenomics/emg-viral-pipeline/compare/v3.2.0...v3.3.0

📋 What's Changed

• Truncate the GFF end boundry for circular prophages by @mberacochea in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/164
• Full Changelog: https://github.com/EBI-Metagenomics/emg-viral-pipeline/compare/v3.1.0...v3.2.0

📋 What's Changed

• Add check for many-Ns by @KateSakharova in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/160
• Chores/gff indexes by @mberacochea in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/162
• Prep for a new release by @mberacochea in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/163
• >[!IMPORTANT]
• >
• > The GFF file in 08-final is compressed now (gz compatible)
• Full Changelog: https://github.com/EBI-Metagenomics/emg-viral-pipeline/compare/v3.0.3...v3.1.0

📋 What's Changed

• Add FAQ in README and a section about FASTA headers and invalid GFF's by @mberacochea in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/155
• Fix parsing script for VS2 records by @KateSakharova in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/154
• Fix/spaces in contignames issue by @KateSakharova in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/156
• Bugfix/transpose on detect output by @KateSakharova in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/157
• Fix the balloon and r_chromomap containers lacking nextflow resource gather tools (i.e. ps) - @mberacochea in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/158
• Full Changelog: https://github.com/EBI-Metagenomics/emg-viral-pipeline/compare/v3.0.2...v3.0.3

📋 What's Changed

• PR by @mberacochea in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/153
• Full Changelog: https://github.com/EBI-Metagenomics/emg-viral-pipeline/compare/v3.0.1...v3.0.2

📋 Changes

• We have decided to remove the CWL version, we dropped it's support in https://github.com/EBI-Metagenomics/emg-viral-pipeline/releases/tag/v2.0.0.
• The pipeline now adhers more to the nf-core standars
• Virify now uses samplesheets input, easier parallelization of assemblies
• Supports user provided proteins as a faa file, if they are provided then the Prodigal step is skipped.
• Upgraded to VirtSorter2, VirSorter1 is still available using flag `--use_virsorter_v1` (we have tested pipeline and realised that VirSorter2 is much slower than VirSorter1. If that is a problem for your execution - stick to VirSorter1, please)
• Output directory re-structure, added flag `--publish_all` to produce expanded output.
• A few fixes on the plots
• Optimised performance when running HMMER against the viphog DB.
• + 1 more

📦 PRs

• Update README.md by @cerebis in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/130
• Re-structure pipeline by @KateSakharova in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/134
• Fix/virsorter2 by @KateSakharova in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/135
• Feature/support protein predictions by @KateSakharova in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/137
• Add annotations for momofy by @KateSakharova in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/138
• pprmeta mcr cache root by @mberacochea in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/136
• Debug/gff writer by @Ales-ibt in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/140
• Fix/prep release by @KateSakharova in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/142
• + 5 more

📋 Changes

• We have decided to remove the CWL version, we dropped it's support in https://github.com/EBI-Metagenomics/emg-viral-pipeline/releases/tag/v2.0.0.
• The pipeline now adhers more to the nf-core standars
• Virify now uses samplesheets input, easier parallelization of assemblies
• Supports user provided proteins as a faa file, if they are provided then the Prodigal step is skipped.
• Upgraded to VirtSorter2, VirSorter 1 is still available using flag `--use_virsorter_v1`
• Output directory re-structure, added flag `--publish_all` to produce expanded output.
• A few fixes on the plots
• Optimised performance when running HMMER against the viphog DB.
• + 1 more

📦 PRs

• Update README.md by @cerebis in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/130
• Re-structure pipeline by @KateSakharova in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/134
• Fix/virsorter2 by @KateSakharova in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/135
• Feature/support protein predictions by @KateSakharova in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/137
• Add annotations for momofy by @KateSakharova in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/138
• pprmeta mcr cache root by @mberacochea in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/136
• Debug/gff writer by @Ales-ibt in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/140
• Fix/prep release by @KateSakharova in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/142
• + 2 more

✨ New Contributors

• @cerebis made their first contribution in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/130
• @fischer-hub made the first contribution with the initial implementation to support VirtSorter2
• Full Changelog: https://github.com/EBI-Metagenomics/emg-viral-pipeline/compare/v2.0.1...v3.0.0

📋 What's Changed

• Fix the Chromomap container. by @mberacochea in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/112
• Fix Chromomap container by @hoelzer in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/114
• remove lsf requirement for ebi profile by @Vkale1 in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/122
• Prase.nf results are optional. by @mberacochea in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/123
• Merge small set of fixes for new release #123 by @mberacochea in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/124

✨ New Contributors

• @Vkale1 made their first contribution in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/122
• Full Changelog: https://github.com/EBI-Metagenomics/emg-viral-pipeline/compare/v2.0.0...v2.0.1

📋 What's Changed

• Adjustment of the voting scheme (see Figure 1) and updated viral taxonomy by @hoelzer and @guille0387 in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/99
• Metadata file v4, also included a warning about the deleted taxa. by @mberacochea in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/106
• Adjustment of the voting scheme and updated viral taxonomy and bugfixes for new release by @hoelzer , @guille0387 and @mberacochea in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/103
• Dropped support for CWL.
• Updates to the README.
• Full Changelog: https://github.com/EBI-Metagenomics/emg-viral-pipeline/compare/v1.1...v2.0.0
• 
• Fig 1 Updated voting scheme.

📋 What's Changed

• Re-build the virsorter container, using one hosted in quay by our team. by @mberacochea in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/94
• Bugfix/issue 92 prophages and gff generation by @Ales-ibt in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/95
• Fasta IDs renaming fixed by @Ales-ibt in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/98
• Bugfix release - PR #94 by @mberacochea in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/97

✨ New Contributors

• @Ales-ibt made their first contribution in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/95
• Full Changelog: https://github.com/EBI-Metagenomics/emg-viral-pipeline/compare/v1.0...v1.1

📋 What's Changed

• First stable release of the pipeline.
• Merged PRs:
• Pprmeta repo fix by @hoelzer in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/75
• Merge DEV by @mberacochea in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/76
• Clean up by @hoelzer in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/78
• Update containers, nf trace compatible now. Some to biocontainers. by @mberacochea in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/81
• CheckV - prophages fixes and post processing gff creation step by @mberacochea in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/80
• Add one simple pytest-workflow test by @mberacochea in https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/89
• + 2 more

📋 Changes

• deactivate the nf tower plugin
• can cause problems on systems that have restricted internet access
• can still be activated by experienced users
• simplify nf version check via `nextflow.config`
• add `CheckV` to the pipeline to get information on quality and completness of contigs that were detected as "viral"

📋 Changes

• length filtering of the input assembly
• detection of potential viral sequences with VirSorter, VirFinder, and PPR-Meta
• classification of potential viruses into high and low confidence sets as well as prophages
• ORF prediction
• protein detection w/ hmmscan using a customized database of virus-specific profile HMMs (so-called ViPhOGs)
• filtering of the hits and taxonomic assignment based on a voting system
• visualization of the results with Krona, Sankey (currently only in the Nextflow pipeline), and ChromoMap (Nextflow)