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RC 3.16.0 #1395

Merged
merged 121 commits into from
Oct 2, 2024
Merged

RC 3.16.0 #1395

merged 121 commits into from
Oct 2, 2024

Commits on Jul 30, 2024

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Commits on Jul 31, 2024

  1. Fix include statements

    egreenberg7 committed Jul 31, 2024
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  2. Fix include statements

    egreenberg7 committed Jul 31, 2024
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Commits on Aug 5, 2024

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Commits on Aug 6, 2024

  1. Fix bracken config

    egreenberg7 committed Aug 6, 2024
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Commits on Aug 7, 2024

  1. Update bracken

    egreenberg7 committed Aug 7, 2024
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  5. Debug input validation

    egreenberg7 committed Aug 7, 2024
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  7. Update changelog

    egreenberg7 committed Aug 7, 2024
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Commits on Aug 9, 2024

  1. Update Kraken2 module

    egreenberg7 committed Aug 9, 2024
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  2. Linting

    egreenberg7 committed Aug 9, 2024
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Commits on Aug 15, 2024

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  3. Debugging

    egreenberg7 committed Aug 15, 2024
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  4. Update usage

    egreenberg7 committed Aug 15, 2024
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Commits on Aug 16, 2024

  1. Fix typo

    egreenberg7 committed Aug 16, 2024
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  2. Update metro map

    egreenberg7 committed Aug 16, 2024
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Commits on Aug 18, 2024

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Commits on Aug 19, 2024

  1. Update schema

    egreenberg7 committed Aug 19, 2024
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  2. Update docs/usage.md

    Co-authored-by: Matthias Zepper <[email protected]>
    egreenberg7 and MatthiasZepper authored Aug 19, 2024
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Commits on Sep 6, 2024

  1. Update main.nf

    pditommaso authored Sep 6, 2024
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Commits on Sep 10, 2024

  1. Update Changelog

    egreenberg7 committed Sep 10, 2024
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  2. Another changelog fix

    egreenberg7 committed Sep 10, 2024
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  3. Update CHANGELOG.md

    pinin4fjords authored Sep 10, 2024
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  4. Linting fix

    egreenberg7 committed Sep 10, 2024
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Commits on Sep 13, 2024

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  2. update CHANGELOG

    maxulysse committed Sep 13, 2024
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  3. update all snapshots

    maxulysse committed Sep 13, 2024
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  5. update half of all snaps

    maxulysse committed Sep 13, 2024
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  7. more snapshots

    maxulysse committed Sep 13, 2024
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  8. update snapshots

    maxulysse committed Sep 13, 2024
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  9. update snapshots

    maxulysse committed Sep 13, 2024
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Commits on Sep 14, 2024

  1. Update CHANGELOG.md

    maxulysse authored Sep 14, 2024
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  2. update snapshots

    maxulysse committed Sep 14, 2024
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Commits on Sep 17, 2024

  1. do not sort output

    maxulysse committed Sep 17, 2024
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  3. sort output by PATH

    maxulysse committed Sep 17, 2024
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  5. update snapshots

    maxulysse committed Sep 17, 2024
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  6. update CHANGELOG

    maxulysse committed Sep 17, 2024
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  7. Update CHANGELOG.md

    Co-authored-by: Jonathan Manning <[email protected]>
    maxulysse and pinin4fjords authored Sep 17, 2024
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  8. Merge pull request #1386 from maxulysse/3.16.0dev

    nf-core pipelines bump-version 3.16.0dev
    maxulysse authored Sep 17, 2024
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  10. snapshot more files

    maxulysse committed Sep 17, 2024
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  11. snapshot more files

    maxulysse committed Sep 17, 2024
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Commits on Sep 18, 2024

  1. feature counts snapshots

    maxulysse committed Sep 18, 2024
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  2. typo

    maxulysse committed Sep 18, 2024
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  3. more snapshots

    maxulysse committed Sep 18, 2024
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  4. more snapshots

    maxulysse committed Sep 18, 2024
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  5. update snapshots

    maxulysse committed Sep 18, 2024
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  6. better regex

    maxulysse committed Sep 18, 2024
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  7. fix regex

    maxulysse committed Sep 18, 2024
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  8. better regex

    maxulysse committed Sep 18, 2024
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Commits on Sep 19, 2024

  1. update snapshot

    maxulysse committed Sep 19, 2024
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  2. code polish

    maxulysse committed Sep 19, 2024
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  3. rescue some snaps

    maxulysse committed Sep 19, 2024
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  4. Apply suggestions from code review

    Co-authored-by: Jonathan Manning <[email protected]>
    maxulysse and pinin4fjords authored Sep 19, 2024
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  5. tiny refactor part I

    maxulysse committed Sep 19, 2024
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  7. update regexes

    maxulysse committed Sep 19, 2024
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  9. simplify regexes

    maxulysse committed Sep 19, 2024
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  10. fix regexes

    maxulysse committed Sep 19, 2024
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  11. Merge conflcits

    egreenberg7 committed Sep 19, 2024
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  13. Update hisat2 patch

    egreenberg7 committed Sep 19, 2024
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  15. Change PR number

    egreenberg7 committed Sep 19, 2024
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  16. Merge pull request #1388 from egreenberg7/dev

    New module: Kraken2/Bracken on Unaligned Sequences for Contamination Detection
    Shaun-Regenbaum authored Sep 19, 2024
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  17. snapshots all filenames

    maxulysse committed Sep 19, 2024
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Commits on Sep 20, 2024

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  2. code polish

    maxulysse committed Sep 20, 2024
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  3. typo

    maxulysse committed Sep 20, 2024
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  6. update CHANGELOG

    maxulysse committed Sep 20, 2024
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  7. Merge pull request #1376 from nf-core/pditommaso-patch-1

    Fix invalid  named parameter syntax
    pinin4fjords authored Sep 20, 2024
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  8. update animated metro_map

    maxulysse committed Sep 20, 2024
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  10. Merge pull request #1389 from maxulysse/update_animate_map

    update animated subway map
    maxulysse authored Sep 20, 2024
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Commits on Sep 23, 2024

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  2. typo

    maxulysse committed Sep 23, 2024
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  4. why was this not commited?

    maxulysse committed Sep 23, 2024
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Commits on Sep 30, 2024

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  2. use url for singularity

    maxulysse committed Sep 30, 2024
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  4. Merge pull request #1393 from maxulysse/patch_registry

    patch bedtools/genomecov to use quay.io to solve issue with nf-core download
    maxulysse authored Sep 30, 2024
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  5. prepare RC 3.15.2

    maxulysse committed Sep 30, 2024
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Commits on Oct 1, 2024

  1. use nft-utils

    maxulysse committed Oct 1, 2024
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  2. update nftignore

    maxulysse committed Oct 1, 2024
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  5. update CHANGELOG

    maxulysse committed Oct 1, 2024
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  6. update nftignore

    maxulysse committed Oct 1, 2024
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  7. update nftignore

    maxulysse committed Oct 1, 2024
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  8. 3.16.0 instead of 3.15.2

    maxulysse committed Oct 1, 2024
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  9. Update CHANGELOG.md

    maxulysse authored Oct 1, 2024
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Commits on Oct 2, 2024

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  2. Merge pull request #1379 from maxulysse/better_snapshots

    Improve pipeline level snapshots
    maxulysse authored Oct 2, 2024
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  4. forgot a merge

    maxulysse committed Oct 2, 2024
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  5. Merge pull request #1394 from maxulysse/prepare_3.15.2

    prepare RC 3.16.0
    maxulysse authored Oct 2, 2024
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  7. Apply suggestions from code review

    Co-authored-by: James A. Fellows Yates <[email protected]>
    maxulysse and jfy133 authored Oct 2, 2024
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