1.2.0 - Ancient Destiny

[1.2.0] - Ancient Destiny [14/01/2025]

• Added Steps - subworkflows are now split into configurable steps.
• Added a .bin output - this will later be used to create modified pretext maps in downstream processes.
• Added .ktab as an output.
• All modules have been updated to remove any Anaconda dependency e.g. the defaults channel.
• Some module versions have been updated too.
• Replaces PyFasta split with seqtk split - fasta split is severely out of date now.
• CICD has been reverted to near the original template - this was changed, originally, to mitigate an error with nextflow being unable to download the large number of containers TreeVal has.
• MerquryFK Module patch to remove memory arg in module as it is unnessecary.
• Modules updated to ensure that version information is being saved.
• BUSCO module now includes the arg --metaeuk by default.
• Changing GENESET to be more userfriendly.
• Adds a JBrowse Only workflow (this will lead to an update to the FULL workflow which can now call JBROWSE_ONLY and RAPID).
• Removing dp24's liberal use of spaces.
• Resource review.

Full Changelog: 1.1.1...1.2.0

v1.1.1 - Ancient Aurora (H1)

[1.1.1] - Ancient Aurora H1 - [2024-07-04]

Our first hotfix for TreeVal, including changing the name of some outputs, correcting some code and fixing an issue with cram files containing multiple RG lines. This will require further fixes in the future, this will include the splitting of the cram file depending on the number of RG lines.

What's Changed

• Reacov bedname by @yumisims in #295
• Generate csv fix by @yumisims in #302
• Dp24 hotfix by @DLBPointon in #298

Full Changelog: 1.1.0...1.1.1

v1.1.0 - Ancient Aurora

[1.1.0] - Ancient Aurora - [2024-04-26]

The second release for sanger-tol, created with the nf-core template.

This builds on the initial release by adding subworkflows which generate Kmer-based coverage tracks and a Kmer spectra graph. There are also a number of updates to the logic used throughout the pipeline, as well as to the resources required by a significant number of modules.

What's Changed

• Updates to the resource allocation methods used by a number of modules in the base.config.
• Added a flag to stop the usage of Juicer.
• Subworkflow to generate a kmer-based coverage track.
• Subworkflow to generate/update a kmer spectra graph.
• Subworkflow to use minimap2 for HiC mapping, if selected.
• Subworkflow to use BWAmem2 for HiC mapping, if selected.
• Subworkflow to ingest Pretext accessory files into the Pretext file, simplifying post-TreeVal data manipulation.
• Updated the logic in use throughout the pipeline.
• Updated the modules.config to include some of the logic, cleaning the code.
• Updated the HiC subworkflow to include subsampling the HiC data for Juicer due to resource requirements with large amounts of data.
• Updated the YAML_INPUT subworkflow, this now contains "flags" to change some software options.
• Updated the data names in the input YAML to reduce confusion.
• Updated software (Pretext{View, Snapshot, Graph}) to allow for use on large genomes with big data.
  • Added associated patch files and CPU architecture files.
• Updated the minimap2 align module to remove samtools view in preference of paftools for our use case.
• Updated the test.yml in line with the above changes.
• Updated the SELFCOMP subworkflow to allow for the parallelisation of the work on large genomes.
• Updated the READ_COVERAGE subworkflow to produce the scaffold-based AVG coverage and STND coverage
• Updated Modules from NF-Core - mostly relates to module structure rather than software.
• Updated the SummaryStats output to include HiC container counts.
• Added -T / -t flags where possible to minimise the use of the /tmp directory.
• Replaced CONCAT_MUMMER with CATCAT for simplicity.
• Removed JUICER from the RAPID entry point.
• Removed the CSI or TBI logic. CSI is now used by default, this simplifies the workflow and enlarges the capacity to handle much larger genomes. The logic block previously required was then moved.
• Added NF-DOWNLOAD to the CI-CD due to an error that causes incomplete downloaded when downloading a number of images at the same time.
• Added the RAPID_TOL entry point which is more geared towards the requirements of Sanger.
• Fix a bug in build_alignment_blocks.py to avoid indexing errors happening in large genomes.
• Change output BEDGRAPH from EXTRACT_TELO module.
• Fix to the telomere output.
• Fix to the SelfComp scripts.

New Contributors

• @gq1 made their first contribution in #186

Contributors

• @DLBPointon
• @yumisims
• @weaglesBio

Full Changelog: 1.0.0...v1.1.0

v1.0.0 – Ancient Atlantis

[1.0.0] - Ancient Atlantis - [2023-09-27]

Initial release of sanger-tol/treeval, created with the nf-core template.

This pipeline allows for the generation of data needed for the high-quality manual curation of genomic assemblies.

What's Changed

• Removing unnecessary code by @DLBPointon in #7
• Generate genome by @DLBPointon in #21
• Digest by @yumisims in #10
• Input refactor by @DLBPointon in #26
• Digest fix by @DLBPointon in #27
• Gene alignment by @DLBPointon in #24
• Changes to conform to linting by @DLBPointon in #29
• Changed input static file system by @DLBPointon in #30
• Self comp merge test by @DLBPointon in #31
• Reorg merge by @DLBPointon in #32
• Main synteny branch by @DLBPointon in #33
• Miniprot p2 by @DLBPointon in #34
• Issue 44 by @weaglesBio in #50
• Issue 43 by @weaglesBio in #49
• Issue 45 by @weaglesBio in #48
• Second round fixes by @DLBPointon in #51
• To fix bug #55 by @DLBPointon in #57
• Create a file object to download it transparently when splitCsv is called by @muffato in #67
• Hap by @yumisims in #68
• Outdir correction by @DLBPointon in #70
• Save file corrections by @DLBPointon in #72
• amended selfcomp process, shrunk the size/number of intermediate files by @yumisims in #73
• Minor fixes, update miniprot params and synteny path by @weaglesBio in #74
• Minor fixes by @DLBPointon in #78
• Longread coverage workflow by @weaglesBio in #82
• Repeat density subworkflow by @DLBPointon in #92
• Local testing by @DLBPointon in #94
• Anc by @DLBPointon in #97
• Anc fixed by @DLBPointon in #100
• Notes for GAP_FINDER by @DLBPointon in #108
• Hic mapping doc by @yumisims in #111
• Busco gene by @yumisims in #118
• Template update by @DLBPointon in #102
• Fixes comma, image links and explainer by @DLBPointon in #120
• Fixes - Modules updated to latest by @DLBPointon in #124
• sanger-tol logo by @muffato in #131
• fixed findHalfcoverage by @yumisims in #130
• Pre tag mm49 by @muffato in #133
• Code suggestions by @muffato in #140
• Pre tag by @DLBPointon in #132
• Tower by @DLBPointon in #142
• Mm49 docs reformat by @DLBPointon in #149
• Adding pretext ingestion docs by @DLBPointon in #145
• Fix genome size by @yumisims in #146
• Refactoring of the test and test_github profiles by @muffato in #152

New Contributors

• @yumisims made their first contribution in #10
• @weaglesBio made their first contribution in #50
• @muffato made their first contribution in #67

Full Changelog: https://github.com/sanger-tol/treeval/commits/v1.0.0