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Test setup nextflow#1462

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ewels wants to merge 61 commits intonf-core:masternf-core/rnaseq:masterfrom ewels:test-setup-nextflowewels/nf-core-rnaseq:test-setup-nextflowCopy head branch name to clipboard

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Commits on Sep 3, 2024

• Add umicollapse as an alternative to umi-tools

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Commits on Sep 4, 2024

• Keep umitools as the default

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Commits on Oct 29, 2024

• add DE_analys folder

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• prettier check

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• Merge branch 'dev' into umicollapse

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• update umicollapse to 1.1.0

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• update CHANGELOG

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Commits on Oct 30, 2024

• change name DE folder

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Commits on Oct 31, 2024

• modify md files

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• prettier check

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Commits on Nov 5, 2024

• actually update umicollapse

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Commits on Nov 6, 2024

• Apply suggestions from code review

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Commits on Nov 7, 2024

• Update docs/usage/DEanalysis/index.md

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• Update docs/usage/DEanalysis/interpretation.md

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• Update docs/usage/DEanalysis/rnaseq.md

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• Update docs/usage/DEanalysis/rnaseq.md

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• Update docs/usage/DEanalysis/rnaseq.md

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• update index.md

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• update images

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• update interpretation

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• update rnaseq

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• update theory

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• update de_rstudio

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• correct formula in theory

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• prettier check

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Commits on Nov 8, 2024

• Merge pull request nf-core#1447 from LorenzoS96/dev

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Commits on Nov 12, 2024

• Merge branch 'dev' into umicollapse

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• [automated] Fix code linting

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Commits on Nov 29, 2024

• Update tests for UMICollapse module.

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• Update umi-tools dedup tests at well.

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• Update tests in subworkflows as well.

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Commits on Dec 2, 2024

• Add linting-enabled preprocessing subworkflow and wire in

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• Update CHANGELOG

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• Add fq/lint

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• Add output previxes for linting

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Commits on Dec 3, 2024

• Tweaks

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• Link in new subworkflow config

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• Let's skip the name validation by default, it seems to be problematic

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• Correct config

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• separate linting reports by directory rather than prefix

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• update schema

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• Add stub to fq lint

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• update docs

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• update snaps

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• exclude lint reports from snapshots

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• update module/ subworkflow

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• Add CI Java fix

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• Fix java ci issue

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• Fix subworkflow test

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• Fix salmon test

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• Merge branch 'swf_rnaseq_prepro_lint' of https://github.com/nf-core/rnaseq into swf_rnaseq_prepro_lint

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• fix changelog and versions

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• Update CHANGELOG.md

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• fix version snap

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• Merge branch 'swf_rnaseq_prepro_lint' of https://github.com/nf-core/rnaseq into swf_rnaseq_prepro_lint

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• Merge pull request nf-core#1461 from nf-core/swf_rnaseq_prepro_lint

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Commits on Dec 4, 2024

• Merge branch 'dev' into umicollapse

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• Restore truncated CHANGELOG.md with 3.0 and prior releases.

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• [automated] Fix code linting

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• Merge pull request nf-core#1369 from siddharthab/umicollapse

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• Make text-only change to confirm tests are broken

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