Tags

Peer review finished, merging non core feature

- parallelized lofreq
- primerstrim_cutoff (like trim_percent_cutoff, but post primers trimming)

Peer review finished, merging non core feature

- Viloca updated
- [Experimental] Preview feature: COJAC output as input to LolliPop

Peer-review for publication

2.99.3 Primers

New features:

 - primer trimming using iVar (by default) or samtools
 - per sample primer protocol using new 4-column sample.tsv format
   (e.g.: for long running projects where protocols change to adapt to
   new variants)

   see: config/README.md#amplicon-protocols

 - `frameshift_deletions_checks`: report on stop codons

Bug fixes:

 - correctly compute runtime requirement within groups

Preview feature:

 - first re-introduction of benchmarking features since V-pipe 2.0
   see: resources/auxiliary_workflows/benchmark/

Documentation:

 - Improved tutorial available inside subdirectory docs/

/!\ Breaking changes:

 - V-pipe now relies on snakemake 7.11 to properly handle 'runtime'
   resource. Consider upgrading !
 - by default the samples' tables `coverage.tsv.gz` and `basecnt.tsv.gz`
   are now 1-based: the first position of the genome is named '1' (as
   standard with genome notations, as in tools like samtools, and as used
   in formats like VCF)
   This can be switched back to 0-based (numbering starts at 0, as
   in python tools like PySAM, and as in the BED format) in config file,
   in section _general_ option _tsvbased_

2.99.2 - Reports and uploads

New features:

 - Mass-importer tools to assist building samples/ directory structure
   from .fastq.gz files.
   (see: utils/README.md)

 - Dehuman: V-pipe can now generate compressed .cram files from the
   raw reads that have been depleted from host (human) reads to assist
   upload to public databases such as, e.g, SRA.
   (see config manual, sections "output" and "dehuman")

 - Diversity: Computation of various diversity indices for the underlying
   samples following the review:
   https://doi.org/10.1016/j.coviro.2021.06.002
   (see config manual, sections "output" and "diversity")

Bugfixes:

 - frameshift_deletions_checks: English language reports now correctly
   covers insertions.

Preview features:

 - a series of tools and features that can be customized to assist in
   uploading results and raw reads to public databases such as ENA.
   (see config manual, sections "output" and "upload",
   see: scripts/prepare_upload_symlinks.sh)

Standardized workflow

 - directory structure follows snakemake workflow catalog's
   standardized usage more closely
 - configuration manual generated automatically from JSON schema
   see: config/config.html

For legacy V-pipe 1.x/2.x users:
 - the new directory structure requires adapting old INI files
   please refer to config/README.md section legacy-v-pipe-1xx2xx-users

NOTE:
 - currently only the analysis of NGS viral data is fully tested and
   guaranteed stable.
 - For other more advanced functionality (e.g., benchmarking) you might
   want to wait until a future release.

Toward a new gen V-pipe

This release incorporate numerous upgrades:

 - Visualisation
 - frameshift_deletions_checks
 - sample consensus fasta generated by bcftools
 - predicthaplo as an additional global haplotype engine
 - support for extremely large cohorts
   (e.g., stats computed per-sample and merged, instead of all BAMs)
 - snakemake _resources_
 - Automatic testing
 - Automatic Docker generation
 - Snakemake standard JSON/YAML configuration
 - `virus_base_config` instead of separate branches (like 'sars-cov2')

This is the last version that:
 - uses a working directory structure that is still similar to
 - and can directly import configurations verbatim from
legacy versions of V-pipe 1.x/2.x and virus-branches (sars-cov2)

NOTE:
- currently only the analysis of NGS viral data is fully tested and
  guaranteed stable.
- For other more advanced functionality (e.g., benchmarking) you might
  want to wait until a future release.

Release of sars-cov2 branch in July 2020

Before rebasing to the latest master

V-pipe 1 release

V-pipe 1.0 release candidate

Rebase onto most recent upstream

V-pipe SARS-CoV2 feature branch snapshot

V-pipe pre-release