[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 https://github.com/sanger-tol/treeval/pull/7 Generate genome by @DLBPointon in https://github.com/sanger-tol/treeval/pull/21 Digest by @yumisims in https://github.com/sanger-tol/treeval/pull/10 Input refactor by @DLBPointon in https://github.com/sanger-tol/treeval/pull/26 Digest fix by @DLBPointon in https://github.com/sanger-tol/treeval/pull/27 Gene alignment by @DLBPointon in https://github.com/sanger-tol/treeval/pull/24 Changes to conform to linting by @DLBPointon in https://github.com/sanger-tol/treeval/pull/29 Changed input static file system by @DLBPointon in https://github.com/sanger-tol/treeval/pull/30 Self comp merge test by @DLBPointon in https://github.com/sanger-tol/treeval/pull/31 Reorg merge by @DLBPointon in https://github.com/sanger-tol/treeval/pull/32 Main synteny branch by @DLBPointon in https://github.com/sanger-tol/treeval/pull/33 Miniprot p2 by @DLBPointon in https://github.com/sanger-tol/treeval/pull/34 Issue 44 by @weaglesBio in https://github.com/sanger-tol/treeval/pull/50 Issue 43 by @weaglesBio in https://github.com/sanger-tol/treeval/pull/49 Issue 45 by @weaglesBio in https://github.com/sanger-tol/treeval/pull/48 Second round fixes by @DLBPointon in https://github.com/sanger-tol/treeval/pull/51 To fix bug #55 by @DLBPointon in https://github.com/sanger-tol/treeval/pull/57 Create a file object to download it transparently when splitCsv is called by @muffato in https://github.com/sanger-tol/treeval/pull/67 Hap by @yumisims in https://github.com/sanger-tol/treeval/pull/68 Outdir correction by @DLBPointon in https://github.com/sanger-tol/treeval/pull/70 Save file corrections by @DLBPointon in https://github.com/sanger-tol/treeval/pull/72 amended selfcomp process, shrunk the size/number of intermediate files by @yumisims in https://github.com/sanger-tol/treeval/pull/73 Minor fixes, update miniprot params and synteny path by @weaglesBio in https://github.com/sanger-tol/treeval/pull/74 Minor fixes by @DLBPointon in https://github.com/sanger-tol/treeval/pull/78 Longread coverage workflow by @weaglesBio in https://github.com/sanger-tol/treeval/pull/82 Repeat density subworkflow by @DLBPointon in https://github.com/sanger-tol/treeval/pull/92 Local testing by @DLBPointon in https://github.com/sanger-tol/treeval/pull/94 Anc by @DLBPointon in https://github.com/sanger-tol/treeval/pull/97 Anc fixed by @DLBPointon in https://github.com/sanger-tol/treeval/pull/100 Notes for GAP_FINDER by @DLBPointon in https://github.com/sanger-tol/treeval/pull/108 Hic mapping doc by @yumisims in https://github.com/sanger-tol/treeval/pull/111 Busco gene by @yumisims in https://github.com/sanger-tol/treeval/pull/118 Template update by @DLBPointon in https://github.com/sanger-tol/treeval/pull/102 Fixes comma, image links and explainer by @DLBPointon in https://github.com/sanger-tol/treeval/pull/120 Fixes - Modules updated to latest by @DLBPointon in https://github.com/sanger-tol/treeval/pull/124 sanger-tol logo by @muffato in https://github.com/sanger-tol/treeval/pull/131 fixed findHalfcoverage by @yumisims in https://github.com/sanger-tol/treeval/pull/130 Pre tag mm49 by @muffato in https://github.com/sanger-tol/treeval/pull/133 Code suggestions by @muffato in https://github.com/sanger-tol/treeval/pull/140 Pre tag by @DLBPointon in https://github.com/sanger-tol/treeval/pull/132 Tower by @DLBPointon in https://github.com/sanger-tol/treeval/pull/142 Mm49 docs reformat by @DLBPointon in https://github.com/sanger-tol/treeval/pull/149 Adding pretext ingestion docs by @DLBPointon in https://github.com/sanger-tol/treeval/pull/145 Fix genome size by @yumisims in https://github.com/sanger-tol/treeval/pull/146 Refactoring of the test and test_github profiles by @muffato in https://github.com/sanger-tol/treeval/pull/152 New Contributors @yumisims made their first contribution in https://github.com/sanger-tol/treeval/pull/10 @weaglesBio made their first contribution in https://github.com/sanger-tol/treeval/pull/50 @muffato made their first contribution in https://github.com/sanger-tol/treeval/pull/67 Full Changelog: https://github.com/sanger-tol/treeval/commits/v1.0.0