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Release v2.0.0#45

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charles-plessy merged 38 commits intomasternf-core/pairgenomealign:masterfrom devnf-core/pairgenomealign:devCopy head branch name to clipboardFeb 5, 2025

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Commits on Jan 20, 2025

• Template update for nf-core/tools version 3.1.2

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Commits on Jan 21, 2025

• Merge branch 'dev' into nf-core-template-merge-3.1.2

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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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• Fix CI with Nextflow 24.12.0-edge

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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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• Lint fixes. Thanks Arthur for the hint on Slack!

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• Remove Debian-style tilde from the version number

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• Merge pull request #37 from nf-core/nf-core-template-merge-3.1.2

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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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• Template update for nf-core/tools version 3.2.0

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• Delete modules/nf-core/fastqc/main.nf

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Commits on Jan 28, 2025

• Merge branch 'dev' into nf-core-template-merge-3.2.0

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• Merge pull request #40 from nf-core/nf-core-template-merge-3.2.0

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• Merge branch 'dev' into milestone_2.0.0

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• Merge pull request #41 from nf-core/master

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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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• Merge pull request #39 from nf-core/milestone_2.0.0

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Commits on Feb 1, 2025

• Mention upgrade to nf-core template 3.2.0

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Commits on Feb 5, 2025

• Fix date in CHANGELOG.md

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