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