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RC 3.16.0#1395

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maxulysse merged 121 commits intomasternf-core/rnaseq:masterfrom devnf-core/rnaseq:devCopy head branch name to clipboardOct 2, 2024

+23,843-18,080

Commits

Commits on Jul 30, 2024

• Install kraken2 and bracken

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• Change nextflow configurations

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• Initial addition of kraken and bracken to pipeline

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Commits on Jul 31, 2024

• Fix include statements

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• Fix include statements

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Commits on Aug 5, 2024

• Include module config files

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• Use presence of kraken_db to determine bracken run, add save params

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• Fix multiqc for Bracken/Kraken

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• Add Bracken/Kraken citations

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Commits on Aug 6, 2024

• Fix bracken config

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Commits on Aug 7, 2024

• Update bracken

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• Adjust multiqc configs for updated bracken

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• Add input validation and update scheme

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• Change default Bracken precision to species

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• Debug input validation

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• Documentation/output image

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• Update changelog

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Commits on Aug 9, 2024

• Update Kraken2 module

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• Linting

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Commits on Aug 15, 2024

• Change to --contaminant_screening param

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• Fixing save unaligned default

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• Debugging

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• Update usage

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• Provide motivation for Kraken2 parameters

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Commits on Aug 16, 2024

• Fix typo

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• Update metro map

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Commits on Aug 18, 2024

• Merge branch 'dev' into dev

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Commits on Aug 19, 2024

• Update schema

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• Update docs/usage.md

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• Change output directory for kraken2/bracken

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Commits on Sep 6, 2024

• Update main.nf

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• Merge branch 'dev' into pditommaso-patch-1

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Commits on Sep 10, 2024

• Update Changelog

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• Another changelog fix

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• Update CHANGELOG.md

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• Linting fix

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Commits on Sep 13, 2024

• make snapshot versions pretty

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• update CHANGELOG

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• update all snapshots

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• Merge branch 'dev' into better_snapshots

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• update half of all snaps

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• Merge branch 'dev' into better_snapshots

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• more snapshots

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• update snapshots

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• update snapshots

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Commits on Sep 14, 2024

• Update CHANGELOG.md

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• update snapshots

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Commits on Sep 17, 2024

• do not sort output

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• Merge branch 'dev' into better_snapshots

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• sort output by PATH

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• nf-core pipelines bump-version 3.16.0dev

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• update snapshots

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• update CHANGELOG

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• Update CHANGELOG.md

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• Merge pull request #1386 from maxulysse/3.16.0dev

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• Merge branch 'dev' into better_snapshots

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• snapshot more files

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• snapshot more files

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Commits on Sep 18, 2024

• feature counts snapshots

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• typo

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• more snapshots

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• more snapshots

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• update snapshots

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• better regex

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• fix regex

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• better regex

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Commits on Sep 19, 2024

• update snapshot

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• code polish

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• rescue some snaps

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• Apply suggestions from code review

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• tiny refactor part I

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• tiny refactor part II - IT IS GROOVY WE CAN SUBSTRACT 🤦

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• update regexes

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• move pipeline regexes in UTILS_PIPELINE

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• simplify regexes

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• fix regexes

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• Merge conflcits

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• Merge branch 'dev' of github.com:egreenberg7/rnaseq into dev

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• Update hisat2 patch

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• (Hopefully) final linting fix

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• Change PR number

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• Merge pull request #1388 from egreenberg7/dev

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• snapshots all filenames

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Commits on Sep 20, 2024

• Merge branch 'dev' into better_snapshots

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• code polish

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• typo

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• Merge branch 'dev' into pditommaso-patch-1

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• Apply suggestions from code review

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• update CHANGELOG

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• Merge pull request #1376 from nf-core/pditommaso-patch-1

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• update animated metro_map

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• Merge branch 'dev' into update_animate_map

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• Merge pull request #1389 from maxulysse/update_animate_map

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• no snpashots of tasks size for workflow for remove_ribo_rna

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• Merge branch 'dev' into better_snapshots

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Commits on Sep 23, 2024

• snapshot number of sucessful tasks

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• typo

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• Update tests/featurecounts_group_type.nf.test

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• why was this not commited?

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Commits on Sep 30, 2024

• patch bedtools/genomecov to use quay.io to solve issue with nf-core download

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• use url for singularity

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• use proper url for singularity

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• Merge pull request #1393 from maxulysse/patch_registry

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• prepare RC 3.15.2

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• update version in snapshots too

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Commits on Oct 1, 2024

• use nft-utils

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• update nftignore

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• Merge branch 'dev' into better_snapshots

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• update pipeline versions in snapshot

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• update CHANGELOG

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• update nftignore

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• update nftignore

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• 3.16.0 instead of 3.15.2

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• Update CHANGELOG.md

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Commits on Oct 2, 2024

• use nft-utils 0.0.2 to get relative path in snapshots

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• Merge pull request #1379 from maxulysse/better_snapshots

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• Merge branch 'dev' into prepare_3.15.2

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• forgot a merge

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• Merge pull request #1394 from maxulysse/prepare_3.15.2

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• Merge branch 'master' into dev

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• Apply suggestions from code review

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