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Milestone 2.0.0#39

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charles-plessy merged 26 commits intodevnf-core/pairgenomealign:devfrom milestone_2.0.0nf-core/pairgenomealign:milestone_2.0.0Copy head branch name to clipboardJan 30, 2025

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Commits on Oct 9, 2024

• Merge pull request #16 from nf-core/dev

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Commits on Dec 18, 2024

• Merge pull request #26 from nf-core/dev

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Commits on Jan 23, 2025

• Do not output the LAST database files, closes #36.

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• Do not output the _many-to-one_ alignment except in --m2m mode.

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• Enforce strictness in seqtk cutn, fixes #18

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• Allow all seeds, closes #34

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• Ignore errors probably caused by no alignments found

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• Update all modules.

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• Fix subworkflows to accept a fixed parameter file. Closes #22

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Commits on Jan 24, 2025

• New option export_aln_to for people who need different formats than MAF.

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• Merge branch 'dev' into milestone_2.0.0

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• Factorise dotplot options and group dotplot config sections

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• pre-commit run --all-files

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Commits on Jan 27, 2025

• Current changelog

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• Update tubemap to version 2.0

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• Documentation updates

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• Merge branch 'milestone_2.0.0' of github.com:nf-core/pairgenomealign into milestone_2.0.0

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• Prepare release 2.0.0

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Commits on Jan 28, 2025

• Merge branch 'dev' into milestone_2.0.0

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Commits on Jan 30, 2025

• Brush up changelog.

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• Update nextflow_schema.json

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• Update nextflow_schema.json

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• Merge branch 'milestone_2.0.0' of github.com:nf-core/pairgenomealign into milestone_2.0.0

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• Mention compression algorithm.

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• Restore unicode quotes.

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• Collect all last/ submodules versions.

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