Small bug fixes release

What's Changed

• Fix the Chromomap container. by @mberacochea in #112
• Fix Chromomap container by @hoelzer in #114
• remove lsf requirement for ebi profile by @Vkale1 in #122
• Prase.nf results are optional. by @mberacochea in #123
• Merge small set of fixes for new release #123 by @mberacochea in #124

New Contributors

• @Vkale1 made their first contribution in #122

Full Changelog: v2.0.0...v2.0.1

v2.0.0

What's Changed

• Adjustment of the voting scheme (see Figure 1) and updated viral taxonomy by @hoelzer and @guille0387 in #99
• Metadata file v4, also included a warning about the deleted taxa. by @mberacochea in #106
• Adjustment of the voting scheme and updated viral taxonomy and bugfixes for new release by @hoelzer , @guille0387 and @mberacochea in #103
• Dropped support for CWL.
• Updates to the README.

Full Changelog: v1.1...v2.0.0

Fig 1 Updated voting scheme.

Minor bugfix release [Nextflow ONLY]

What's Changed

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

New Contributors

• @Ales-ibt made their first contribution in #95

Full Changelog: v1.0...v1.1

v1.0

What's Changed

First stable release of the pipeline.

Merged PRs:

• Pprmeta repo fix by @hoelzer in #75
• Merge DEV by @mberacochea in #76
• Clean up by @hoelzer in #78
• Update containers, nf trace compatible now. Some to biocontainers. by @mberacochea in #81
• CheckV - prophages fixes and post processing gff creation step by @mberacochea in #80
• Add one simple pytest-workflow test by @mberacochea in #89
• 1.0 release PR :) by @mberacochea in #88

Full Changelog: v0.4.0...v1.0

v0.4.0

• 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"

Third RC

This is a third release candidate of the EBI metagenomics virus detection and classification pipeline.

This RC contains updates to the software required to run the pipeline, nextflow version upgrade and cwl-toil version upgrade

Reproducible release: no PPR-Meta

Older versions of the pipeline were run without PPR-Meta as a third tool for virus prediction.

To increase reproducibility for such older analyses, this release deactivates virus prediction via PPR-Meta to represent a reproducible code version based only on the initial viral contig predictions with VirSorter and VirFinder.

Second RC

This is a second release candidate of the EBI metagenomics virus detection and classification pipeline.

Initial release

This is a first release candidate of the EBI metagenomics virus detection and classification pipeline.

The pipeline is implemented in Nextflow and CWL based on the same core Python and Shell scripts and Docker containers.

The pipeline features

• 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)