Prepare 3.0.0#127
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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
jfy133
approved these changes
Jun 24, 2026
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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This prepares the
3.0.0release.The most important breaking changes are the upgrade of LAST and the change of some default alignment parameters, as they alter the alignment results.
Since this triggers a major version bump, I took the opportunity to add more minor breaking changes that modify file names or paths, update the CRAM encoding version, and make bigger plots. Nextflow
26.04is now required. Users who can not upgrade to Nextflow26.04can still access most the most important recent developments (like the multi-genome CRAM files) in the previous version of the pipeline (2.3.0).Breaking changes_alnand_plt.samtools(CRAM v3.1 as ofsamtools1.23.1) (#86).--gapsymand--matsymtolast-train(#91).YASStoRY128(#121).cutntotargetgenome(#126).Fixed26.04"strict syntax" (#120).last/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).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).