v3.0.0 "Tokoroten" - [June 26th 2026]#130
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Closes #118 `--dotplot_width` now defaults to 1200 instead 1000 (which is a bit small on modern screens). `--rot1=v` is passed to last-dotplot to ensure that more sequence names from the _target_ genome are readable. This can be reverted with `--dotplot_options='--rot1=h'`.
…atsym` to `last-train`. Closes: #91
Closes #120
This opens the exciting possibility of aligning many targets to many queries in the future, as opposed to just a single target and a single query. Also thanks to this the `main.nf` file is a pristine copy of the version in TEMPLATE branch, which will simplify future merges. Closes #119
Plus manual editing of README.md and nf-core rocrate
…nary distance indices Closes #102
This makes it smoother for reaching one file type when having the other name in the clipboard: only need to care about changing the file name suffix.
Closes #122 This open the door to a future option allowing the user to align reads to genomes using LAST, maybe in version 3.1. Adding it now as an Easter Egg as it will reduce the delta between the nf-core version and the branch that I have in private to test future developments. Alignment of reads to genomes was present in the ancestor of this pipeline, https://github.com/oist/plessy_pairwiseGenomeComparison
This simplifies its output, allowing us to simplify the main workflow. This also opens the door to BCF output support.
wave --freeze --conda 'bioconda::last=1651' --conda 'bioconda::samtools=1.23.1' --conda 'bioconda::bcftools=1.23.1' --conda 'conda-forge::open-fonts=0.7.0' --conda 'conda-forge::gzip=1.14' --conda 'conda-forge::bzip2=1.0.8' --conda 'conda-forge::xz=5.8.3'
Converting pairwise genome alignment to BCF is kind of heretic, but seems to work. This said, the feature should be considered experimental at least in this release, with no guarantee that the results make sense or are reproducible in the next minor release. Closes: #82
Closes #115
… MultiQC in version `2.3.0`. Closes #124
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Prepare 3.0.0
… of the _target_ genome when both strands are indexed. Closes: #128
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
Fix erroneous doubling of the reported length and number of sequences
jfy133
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Looks great. A single comment on input file suffixes.
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v3.0.0 "Tokoroten" - [June 26th 2026]
Breaking changes_alnand_plt.samtools(CRAM v3.1 as ofsamtools1.23.1) (#86).--gapsymand--matsymtolast-train(#91).YASStoRY4(#121).cutntotargetgenome(#126).Addedlast/mafconvertto allow BCF output, and updated the module diffs so that the shared container also includes BCFtools. BCF output is experimental and output may change in minor revisions of the pipeline (#82).Fixed26.04"strict syntax" (#120).2.3.0(#124).DependenciesLASTBCFTOOLSSAMTOOLSMultiQCPR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).