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New module: Kraken2/Bracken on Unaligned Sequences for Contamination Detection #1351

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Closed

New module: Kraken2/Bracken on Unaligned Sequences for Contamination Detection #1351

wants to merge 242 commits into from

Commits on Jul 3, 2024

  1. stub for align_star + a single snapshot match per test

    @maxulysse
    maxulysse committed Jul 3, 2024
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  2. add stubs + code polish + Harshil align

    @maxulysse
    maxulysse committed Jul 3, 2024
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  3. add stub

    @maxulysse
    maxulysse committed Jul 3, 2024
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  4. update all nf-core modules and subworkflows and do not include tags

    @maxulysse
    maxulysse committed Jul 3, 2024
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  5. simplify snapshot for stub

    @maxulysse
    maxulysse committed Jul 3, 2024
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  6. add stubs for subworkflow local quantify_rsem

    @maxulysse
    maxulysse committed Jul 3, 2024
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  7. update default snapshot

    @maxulysse
    maxulysse committed Jul 3, 2024
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Commits on Jul 4, 2024

  1. add plugin

    @maxulysse
    maxulysse committed Jul 4, 2024
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  2. update all subworkflows

    @maxulysse
    maxulysse committed Jul 4, 2024
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  3. do not snapshot fastq in stub

    @maxulysse
    maxulysse committed Jul 4, 2024
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  4. pipeline level stub

    @maxulysse
    maxulysse committed Jul 4, 2024
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  5. fix stub test for prepare_genome

    @maxulysse
    maxulysse committed Jul 4, 2024
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  6. update all subworkflows

    @maxulysse
    maxulysse committed Jul 4, 2024
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Commits on Jul 5, 2024

  1. correctly align

    @maxulysse
    maxulysse committed Jul 5, 2024
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Commits on Jul 9, 2024

  1. update all modules

    @maxulysse
    maxulysse committed Jul 9, 2024
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Commits on Jul 11, 2024

  1. use seqera containers

    @maxulysse
    maxulysse committed Jul 11, 2024
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Commits on Jul 12, 2024

  1. Merge branch 'dev' into stubs_everywhere

    @maxulysse
    maxulysse committed Jul 12, 2024
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  2. update all modules/subworkflows + remove tags

    @maxulysse
    maxulysse committed Jul 12, 2024
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  3. update snapshot

    @maxulysse
    maxulysse committed Jul 12, 2024
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Commits on Jul 16, 2024

  1. Merge branch 'dev' into stubs_everywhere

    @maxulysse
    maxulysse committed Jul 16, 2024
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Commits on Jul 22, 2024

  1. Merge branch 'dev' into stubs_everywhere

    @maxulysse
    maxulysse committed Jul 22, 2024
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  2. update nf-test to 0.9.0

    @maxulysse
    maxulysse committed Jul 22, 2024
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  3. sort

    @maxulysse
    maxulysse committed Jul 22, 2024
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  4. update all modules/subworkflows + remove tags

    @maxulysse
    maxulysse committed Jul 22, 2024
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  5. remove tags

    @maxulysse
    maxulysse committed Jul 22, 2024
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  6. keep card 3.1.1 that does not break CI due to weird RG

    @maxulysse
    maxulysse committed Jul 22, 2024
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  7. update snapshot

    @maxulysse
    maxulysse committed Jul 22, 2024
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  8. update snapshot

    @maxulysse
    maxulysse committed Jul 22, 2024
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  9. update all modules + subworkflows / remove tags + path markduplicates

    @maxulysse
    maxulysse committed Jul 22, 2024
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  10. update snapshots

    @maxulysse
    maxulysse committed Jul 22, 2024
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  11. update stringtie_stringtie

    @maxulysse
    maxulysse committed Jul 22, 2024
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  12. update snapshots for fastq_align_hisat2

    @maxulysse
    maxulysse committed Jul 22, 2024
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  13. add proper stubs and tests for local star_*_igenomes modules

    @maxulysse
    maxulysse committed Jul 22, 2024
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Commits on Jul 30, 2024

  1. Install kraken2 and bracken

    @egreenberg7
    egreenberg7 committed Jul 30, 2024
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  2. Change nextflow configurations

    @egreenberg7
    egreenberg7 committed Jul 30, 2024
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  3. Initial addition of kraken and bracken to pipeline

    @egreenberg7
    egreenberg7 committed Jul 30, 2024
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Commits on Jul 31, 2024

  1. Fix include statements

    @egreenberg7
    egreenberg7 committed Jul 31, 2024
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  2. Fix include statements

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

  1. Include module config files

    @egreenberg7
    egreenberg7 committed Aug 5, 2024
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  2. Use presence of kraken_db to determine bracken run, add save params

    @egreenberg7
    egreenberg7 committed Aug 5, 2024
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  3. Fix multiqc for Bracken/Kraken

    @egreenberg7
    egreenberg7 committed Aug 5, 2024
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  4. Add Bracken/Kraken citations

    @egreenberg7
    egreenberg7 committed Aug 5, 2024
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Commits on Aug 6, 2024

  1. Fix bracken config

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

  1. Update bracken

    @egreenberg7
    egreenberg7 committed Aug 7, 2024
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  2. Adjust multiqc configs for updated bracken

    @egreenberg7
    egreenberg7 committed Aug 7, 2024
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  3. Add input validation and update scheme

    @egreenberg7
    egreenberg7 committed Aug 7, 2024
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  4. Change default Bracken precision to species

    @egreenberg7
    egreenberg7 committed Aug 7, 2024
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  5. Debug input validation

    @egreenberg7
    egreenberg7 committed Aug 7, 2024
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  6. Documentation/output image

    @egreenberg7
    egreenberg7 committed Aug 7, 2024
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  7. Update changelog

    @egreenberg7
    egreenberg7 committed Aug 7, 2024
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  8. Try multiqc fixes

    @pinin4fjords
    pinin4fjords committed Aug 7, 2024
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Commits on Aug 8, 2024

  1. Fix rename patterns

    @pinin4fjords
    pinin4fjords committed Aug 8, 2024
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  2. Import tsv func from nf-core subworkflow

    @pinin4fjords
    pinin4fjords committed Aug 8, 2024
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  3. Better define ordering

    @pinin4fjords
    pinin4fjords committed Aug 8, 2024
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  4. Add new header, define some sections, reinstate trimming status repor… 

    …ting
    @pinin4fjords
    pinin4fjords committed Aug 8, 2024
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Commits on Aug 9, 2024

  1. Update Kraken2 module

    @egreenberg7
    egreenberg7 committed Aug 9, 2024
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  2. Linting

    @egreenberg7
    egreenberg7 committed Aug 9, 2024
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  3. Fix up methods and versions passed to MultiQC

    @pinin4fjords
    pinin4fjords committed Aug 9, 2024
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  4. Attempt a rational fixed ordering of sections

    @pinin4fjords
    pinin4fjords committed Aug 9, 2024
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  5. Temp fix pending suworkflow update

    @pinin4fjords
    pinin4fjords committed Aug 9, 2024
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  6. update subworkflow from nf-core

    @pinin4fjords
    pinin4fjords committed Aug 9, 2024
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  7. update changelog

    @pinin4fjords
    pinin4fjords committed Aug 9, 2024
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Commits on Aug 15, 2024

  1. Change to --contaminant_screening param

    @egreenberg7
    egreenberg7 committed Aug 15, 2024
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  2. Fixing save unaligned default

    @egreenberg7
    egreenberg7 committed Aug 15, 2024
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  3. Debugging

    @egreenberg7
    egreenberg7 committed Aug 15, 2024
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  4. Update usage

    @egreenberg7
    egreenberg7 committed Aug 15, 2024
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  5. Provide motivation for Kraken2 parameters

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

  1. Merge branch 'dev' into stubs_everywhere

    @maxulysse
    maxulysse committed Aug 16, 2024
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  2. proper sha for module bedtools/genomecov

    @maxulysse
    maxulysse committed Aug 16, 2024
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  3. update samtools/stats module + rm tags

    @maxulysse
    maxulysse committed Aug 16, 2024
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  4. Merge branch 'dev' into harmonize_new_for_multiqc

    @pinin4fjords
    pinin4fjords committed Aug 16, 2024
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  5. Fix typo

    @egreenberg7
    egreenberg7 committed Aug 16, 2024
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  6. Update metro map

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

  1. Merge branch 'dev' into dev

    @Shaun-Regenbaum
    Shaun-Regenbaum committed Aug 18, 2024
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Commits on Aug 19, 2024

  1. Update schema

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

    Co-authored-by: Matthias Zepper <[email protected]>
    @egreenberg7 @MatthiasZepper
    egreenberg7 and MatthiasZepper committed Aug 19, 2024
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  3. Update multiqc for prefix usage

    @pinin4fjords
    pinin4fjords committed Aug 19, 2024
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  4. Change output directory for kraken2/bracken

    @egreenberg7
    egreenberg7 committed Aug 19, 2024
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  5. tiny updates on subway map

    @maxulysse
    maxulysse committed Aug 19, 2024
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  6. realign

    @maxulysse
    maxulysse committed Aug 19, 2024
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  7. tiny fixes

    @maxulysse
    maxulysse committed Aug 19, 2024
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  8. update CHANGELOG

    @maxulysse
    maxulysse committed Aug 19, 2024
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  9. Update CHANGELOG.md

    @maxulysse
    maxulysse committed Aug 19, 2024
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Commits on Aug 20, 2024

  1. Bump multiqc

    @pinin4fjords
    pinin4fjords committed Aug 20, 2024
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  2. Unset multiqc prefix for testing

    @pinin4fjords
    pinin4fjords committed Aug 20, 2024
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  3. Merge pull request nf-core#1355 from maxulysse/subway_map_one_more_time 

    Fix curves in subway map
    @maxulysse
    maxulysse committed Aug 20, 2024
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  4. Merge branch 'dev' into harmonize_new_for_multiqc

    @pinin4fjords
    pinin4fjords committed Aug 20, 2024
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  5. Update workflows/rnaseq/main.nf 

    Co-authored-by: Adam Talbot <[email protected]>
    @pinin4fjords @adamrtalbot
    pinin4fjords and adamrtalbot committed Aug 20, 2024
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  6. Merge pull request nf-core#1352 from nf-core/harmonize_new_for_multiqc 

    Assorted fixes to MultiQC usage
    @pinin4fjords
    pinin4fjords committed Aug 20, 2024
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  7. Merge branch 'dev' into stubs_everywhere

    @maxulysse
    maxulysse committed Aug 20, 2024
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  8. clean up stub tests

    @maxulysse
    maxulysse committed Aug 20, 2024
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  9. Fix anchor issue in multiqc

    @pinin4fjords
    pinin4fjords committed Aug 20, 2024
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  10. Update CHANGELOG.md

    @pinin4fjords
    pinin4fjords committed Aug 20, 2024
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  11. Merge pull request nf-core#1357 from nf-core/fix_anchor_issue 

    Work around anchor issue in multiqc
    @pinin4fjords
    pinin4fjords committed Aug 20, 2024
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  12. Merge branch 'dev' into stubs_everywhere

    @maxulysse
    maxulysse committed Aug 20, 2024
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  13. update CHANGELOG

    @maxulysse
    maxulysse committed Aug 20, 2024
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  14. Animate subway map

    @maxulysse
    maxulysse committed Aug 20, 2024
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  15. update snapshot

    @maxulysse
    maxulysse committed Aug 20, 2024
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Commits on Aug 21, 2024

  1. update snapshot

    @maxulysse
    maxulysse committed Aug 21, 2024
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  2. Merge pull request nf-core#1335 from maxulysse/stubs_everywhere 

    Adding stubs at all level
    @maxulysse
    maxulysse committed Aug 21, 2024
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  3. Update test_full.config to restore a static URI for megatests

    @pinin4fjords
    pinin4fjords committed Aug 21, 2024
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  4. Update CHANGELOG.md

    @pinin4fjords
    pinin4fjords committed Aug 21, 2024
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  5. use permalink

    @pinin4fjords
    pinin4fjords committed Aug 21, 2024
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  6. Same for minimal tests

    @pinin4fjords
    pinin4fjords committed Aug 21, 2024
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  7. Update CHANGELOG.md

    @pinin4fjords
    pinin4fjords committed Aug 21, 2024
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  8. fix double reference

    @pinin4fjords
    pinin4fjords committed Aug 21, 2024
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  9. Merge branch 'static_uri_megatests' of github.com:nf-core/rnaseq into… 

    … static_uri_megatests
    @pinin4fjords
    pinin4fjords committed Aug 21, 2024
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  10. Fix input

    @pinin4fjords
    pinin4fjords committed Aug 21, 2024
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  11. Merge pull request nf-core#1358 from nf-core/static_uri_megatests 

    Update test_full.config to restore a static URI for megatests
    @pinin4fjords
    pinin4fjords committed Aug 21, 2024
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  12. Revert multiqc workaround due to fix

    @pinin4fjords
    pinin4fjords committed Aug 21, 2024
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  13. Update changelog

    @pinin4fjords
    pinin4fjords committed Aug 21, 2024
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  14. Update changelog

    @pinin4fjords
    pinin4fjords committed Aug 21, 2024
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  15. snapshot all files contents by default

    @maxulysse
    maxulysse committed Aug 21, 2024
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  16. animate metro map

    @maxulysse
    maxulysse committed Aug 21, 2024
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  17. Merge branch 'dev' into moar_snapshots

    @maxulysse
    maxulysse committed Aug 21, 2024
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  18. Merge branch 'dev' into animate_subway

    @maxulysse
    maxulysse committed Aug 21, 2024
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Commits on Aug 22, 2024

  1. fix MultiQC paths

    @maxulysse
    maxulysse committed Aug 22, 2024
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  2. Install properly

    @pinin4fjords
    pinin4fjords committed Aug 22, 2024
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  3. Merge pull request nf-core#1359 from nf-core/revert_multiqc_workaround 

    Revert multiqc workaround
    @pinin4fjords
    pinin4fjords committed Aug 22, 2024
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  4. Merge branch 'dev' into animate_subway

    @maxulysse
    maxulysse committed Aug 22, 2024
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  5. Tidy up multiqc test config

    @pinin4fjords
    pinin4fjords committed Aug 22, 2024
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  6. Add module config

    @pinin4fjords
    pinin4fjords committed Aug 22, 2024
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  7. Update changelog

    @pinin4fjords
    pinin4fjords committed Aug 22, 2024
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  8. Install changes from modules

    @pinin4fjords
    pinin4fjords committed Aug 22, 2024
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  9. Merge pull request nf-core#1362 from nf-core/multiqc_test_config 

    Move multiqc module prefix for nf-test to module
    @maxulysse
    maxulysse committed Aug 22, 2024
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  10. update test and snapshot

    @maxulysse
    maxulysse committed Aug 22, 2024
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  11. Merge branch 'dev' into moar_snapshots

    @maxulysse
    maxulysse committed Aug 22, 2024
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  12. update MultiQC paths

    @maxulysse
    maxulysse committed Aug 22, 2024
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  13. sort files

    @maxulysse
    maxulysse committed Aug 22, 2024
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  14. update test and snapshot

    @maxulysse
    maxulysse committed Aug 22, 2024
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  15. update test and snapshot

    @maxulysse
    maxulysse committed Aug 22, 2024
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  16. more snapshots

    @maxulysse
    maxulysse committed Aug 22, 2024
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  17. update test and snapshot

    @maxulysse
    maxulysse committed Aug 22, 2024
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  18. update CHANGELOG

    @maxulysse
    maxulysse committed Aug 22, 2024
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  19. update test and snapshot

    @maxulysse
    maxulysse committed Aug 22, 2024
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  20. update test and snapshot

    @maxulysse
    maxulysse committed Aug 22, 2024
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  21. revert update CHANGELOG

    @maxulysse
    maxulysse committed Aug 22, 2024
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  22. update test and snapshot

    @maxulysse
    maxulysse committed Aug 22, 2024
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  23. Merge branch 'dev' into animate_subway

    @maxulysse
    maxulysse committed Aug 22, 2024
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  24. update CHANGELOG

    @maxulysse
    maxulysse committed Aug 22, 2024
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  25. text to path

    @maxulysse
    maxulysse committed Aug 22, 2024
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  26. typo

    @maxulysse
    maxulysse committed Aug 22, 2024
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  27. more snapshots

    @maxulysse
    maxulysse committed Aug 22, 2024
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  28. text to path

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    maxulysse committed Aug 22, 2024
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Commits on Aug 23, 2024

  1. update snapshots

    @maxulysse
    maxulysse committed Aug 23, 2024
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  2. fastqc html are not stable

    @maxulysse
    maxulysse committed Aug 23, 2024
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  3. update tests and snapshots

    @maxulysse
    maxulysse committed Aug 23, 2024
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  4. update tests and snapshots

    @maxulysse
    maxulysse committed Aug 23, 2024
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  5. update tests and snapshots

    @maxulysse
    maxulysse committed Aug 23, 2024
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  6. update tests and snapshots

    @maxulysse
    maxulysse committed Aug 23, 2024
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  7. kallisto

    @maxulysse
    maxulysse committed Aug 23, 2024
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  8. Add link to static version

    @maxulysse
    maxulysse committed Aug 23, 2024
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  9. kallisto with snapshots

    @maxulysse
    maxulysse committed Aug 23, 2024
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  10. kallisto updated snapshots

    @maxulysse
    maxulysse committed Aug 23, 2024
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  11. min_mapped_reads snapshots

    @maxulysse
    maxulysse committed Aug 23, 2024
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  12. min_mapped_reads better snapshots

    @maxulysse
    maxulysse committed Aug 23, 2024
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  13. fix stub snap

    @maxulysse
    maxulysse committed Aug 23, 2024
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  14. remove_ribo_rna snapshots

    @maxulysse
    maxulysse committed Aug 23, 2024
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Commits on Aug 26, 2024

  1. update remove_ribo_rna snapshots

    @maxulysse
    maxulysse committed Aug 26, 2024
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  2. Merge pull request nf-core#1361 from maxulysse/animate_subway 

    Animate subway map
    @maxulysse
    maxulysse committed Aug 26, 2024
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  3. Merge branch 'dev' into moar_snapshots

    @maxulysse
    maxulysse committed Aug 26, 2024
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  4. salmon snapshots + update moar snapshots

    @maxulysse
    maxulysse committed Aug 26, 2024
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  5. skip_qc snapshots

    @maxulysse
    maxulysse committed Aug 26, 2024
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  6. update tests and snapshots

    @maxulysse
    maxulysse committed Aug 26, 2024
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  7. fix tests and snapshots

    @maxulysse
    maxulysse committed Aug 26, 2024
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  8. skip_trimming test and snapshots

    @maxulysse
    maxulysse committed Aug 26, 2024
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  9. update test and snapshots

    @maxulysse
    maxulysse committed Aug 26, 2024
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  10. fix linting + star_rsem tests and snapshots

    @maxulysse
    maxulysse committed Aug 26, 2024
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  11. update CHANGELOG

    @maxulysse
    maxulysse committed Aug 26, 2024
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  12. fix merge conflicts

    @maxulysse
    maxulysse committed Aug 26, 2024
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  13. update tests

    @maxulysse
    maxulysse committed Aug 26, 2024
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  14. update tests and snapshots

    @maxulysse
    maxulysse committed Aug 26, 2024
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Commits on Aug 27, 2024

  1. Merge pull request nf-core#1360 from maxulysse/moar_snapshots 

    Snapshot all files (content or file name when not stable)
    @maxulysse
    maxulysse committed Aug 27, 2024
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Commits on Aug 28, 2024

  1. update fastqc module

    @maxulysse
    maxulysse committed Aug 28, 2024
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  2. update utils subworkflows

    @maxulysse
    maxulysse committed Aug 28, 2024
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  3. use proper script for dupradar

    @maxulysse
    maxulysse committed Aug 28, 2024
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  4. no need for tags

    @maxulysse
    maxulysse committed Aug 28, 2024
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  5. no need for tags

    @maxulysse
    maxulysse committed Aug 28, 2024
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  6. update CHANGELOG

    @maxulysse
    maxulysse committed Aug 28, 2024
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  7. Merge pull request nf-core#1363 from maxulysse/last_fix_before_3-15 

    Fixing failing tests and updating modules once more
    @maxulysse
    maxulysse committed Aug 28, 2024
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Commits on Aug 29, 2024

  1. Clarify docs on different tximport count files

    @pmoris
    pmoris committed Aug 29, 2024
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  2. Clarify design formula and blind dispersion estimation

    @pmoris
    pmoris committed Aug 29, 2024
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Commits on Sep 3, 2024

  1. Update docs/output.md

    @pinin4fjords
    pinin4fjords committed Sep 3, 2024
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  2. Update docs/output.md

    @pinin4fjords
    pinin4fjords committed Sep 3, 2024
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  3. Update output.md 

    Clarify output files:
- add gene_lengths description
- clarify that scaled output files contain estimated counts from abundances
    @pmoris
    pmoris committed Sep 3, 2024
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  4. Update CHANGELOG.md

    @pinin4fjords
    pinin4fjords committed Sep 3, 2024
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  5. Remove restatement of params defaults

    @pinin4fjords
    pinin4fjords committed Sep 3, 2024
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  6. Update CHANGELOG.md

    @pinin4fjords
    pinin4fjords committed Sep 3, 2024
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  7. Apply suggestions from code review

    @pinin4fjords
    pinin4fjords committed Sep 3, 2024
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  8. Merge pull request nf-core#1367 from pmoris/clarify-deseq2-qc 

    Clarify design formula and blind dispersion estimation
    @pinin4fjords
    pinin4fjords committed Sep 3, 2024
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  9. Merge branch 'dev' into improve-docs-count-files

    @pinin4fjords
    pinin4fjords committed Sep 3, 2024
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  10. Merge pull request nf-core#1366 from pmoris/improve-docs-count-files 

    Clarify docs on different tximport count files
    @pinin4fjords
    pinin4fjords committed Sep 3, 2024
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  11. Bump versions

    @pinin4fjords
    pinin4fjords committed Sep 3, 2024
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  12. Bump modules

    @pinin4fjords
    pinin4fjords committed Sep 3, 2024
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  13. Remove tags from tests 

    Co-authored-by: Maxime U Garcia <[email protected]>
    @pinin4fjords @maxulysse
    pinin4fjords and maxulysse committed Sep 3, 2024
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  14. Fix version in snapshot

    @pinin4fjords
    pinin4fjords committed Sep 3, 2024
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  15. Merge branch 'prerelease_3.15.0_fixes' of github.com:nf-core/rnaseq i… 

    …nto prerelease_3.15.0_fixes
    @pinin4fjords
    pinin4fjords committed Sep 3, 2024
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Commits on Sep 4, 2024

  1. Merge pull request nf-core#1370 from nf-core/prerelease_3.15.0_fixes 

    Bump versions for 3.15.0
    @pinin4fjords
    pinin4fjords committed Sep 4, 2024
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  2. Apply Maxime's suggestions to changelog

    @pinin4fjords
    pinin4fjords committed Sep 4, 2024
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  3. Add new PRs to changelog

    @pinin4fjords
    pinin4fjords committed Sep 4, 2024
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  4. Bump CI

    @pinin4fjords
    pinin4fjords committed Sep 4, 2024
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  5. Merge pull request nf-core#1371 from nf-core/maxime_changelog_changes 

    Apply Maxime's changelog edits
    @pinin4fjords
    pinin4fjords committed Sep 4, 2024
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  6. Bump tximeta/tximport for gene table rownames fix

    @pinin4fjords
    pinin4fjords committed Sep 4, 2024
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  7. Update changelog

    @pinin4fjords
    pinin4fjords committed Sep 4, 2024
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  8. Merge pull request nf-core#1372 from nf-core/bump_tximport_gene_names 

    Bump tximeta/tximport for gene table row names fix
    @pinin4fjords
    pinin4fjords committed Sep 4, 2024
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Commits on Sep 5, 2024

  1. Merge pull request nf-core#1258 from nf-core/dev 

    [skip ci] Dev -> Master for 3.15.0
    @pinin4fjords
    pinin4fjords committed Sep 5, 2024
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  2. Bump versions for next release

    @pinin4fjords
    pinin4fjords committed Sep 5, 2024
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  3. Bump CI

    @pinin4fjords
    pinin4fjords committed Sep 5, 2024
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  4. Update CHANGELOG.md 

    Co-authored-by: Maxime U Garcia <[email protected]>
    @pinin4fjords @maxulysse
    pinin4fjords and maxulysse committed Sep 5, 2024
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  5. Update changelog

    @pinin4fjords
    pinin4fjords committed Sep 5, 2024
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  6. Merge pull request nf-core#1374 from nf-core/postrelese_3.15.0 

    Bump pipeline version to 3.16.0dev
    @pinin4fjords
    pinin4fjords committed Sep 5, 2024
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Commits on Sep 10, 2024

  1. Update Changelog

    @egreenberg7
    egreenberg7 committed Sep 10, 2024
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  2. Another changelog fix

    @egreenberg7
    egreenberg7 committed Sep 10, 2024
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  3. Linting fix

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

  1. Fix R module name-mangling issues

    @pinin4fjords
    pinin4fjords committed Sep 13, 2024
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  2. Bump changelog

    @pinin4fjords
    pinin4fjords committed Sep 13, 2024
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  3. Merge pull request nf-core#1380 from nf-core/fix_tximport_summarizede… 

    …xperiment

Fix issues with R modules changing sample names
    @pinin4fjords
    pinin4fjords committed Sep 13, 2024
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  4. update all modules

    @maxulysse
    maxulysse committed Sep 13, 2024
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  5. update CHANGELOG

    @maxulysse
    maxulysse committed Sep 13, 2024
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  6. better patch of picard md

    @maxulysse
    maxulysse committed Sep 13, 2024
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  7. include conda changes to local modules too

    @maxulysse
    maxulysse committed Sep 13, 2024
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  8. slight fixes for rnaseq prepro

    @pinin4fjords
    pinin4fjords committed Sep 13, 2024
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  9. Merge pull request nf-core#1381 from maxulysse/massive_conda_update 

    Massive conda modules update
    @maxulysse
    maxulysse committed Sep 13, 2024
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  10. Remove chunk duplicated from subworkflow

    @pinin4fjords
    pinin4fjords committed Sep 13, 2024
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  11. Try from branch

    @pinin4fjords
    pinin4fjords committed Sep 13, 2024
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Commits on Sep 16, 2024

  1. Merge branch 'dev' into rnaseq_propro_trimfail_fix

    @pinin4fjords
    pinin4fjords committed Sep 16, 2024
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  2. install subworkflow from master

    @pinin4fjords
    pinin4fjords committed Sep 16, 2024
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  3. Update changelog

    @pinin4fjords
    pinin4fjords committed Sep 16, 2024
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  4. Merge pull request nf-core#1382 from nf-core/rnaseq_propro_trimfail_fix 

    Slight fixes for rnaseq preprocessing
    @pinin4fjords
    pinin4fjords committed Sep 16, 2024
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  5. Bump versions

    @pinin4fjords
    pinin4fjords committed Sep 16, 2024
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  6. update changelog

    @pinin4fjords
    pinin4fjords committed Sep 16, 2024
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  7. Merge pull request nf-core#1383 from nf-core/prerelease_3.15.1_fixes 

    Prerelease 3.15.1 version bumps
    @pinin4fjords
    pinin4fjords committed Sep 16, 2024
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  8. Merge branch 'master' into master_merge

    @pinin4fjords
    pinin4fjords committed Sep 16, 2024
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  9. Merge pull request nf-core#1385 from nf-core/master_merge 

    Master merge
    @pinin4fjords
    pinin4fjords committed Sep 16, 2024
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Commits on Sep 17, 2024

  1. nf-core pipelines bump-version 3.16.0dev

    @maxulysse
    maxulysse committed Sep 17, 2024
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  2. update CHANGELOG

    @maxulysse
    maxulysse committed Sep 17, 2024
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  3. Update CHANGELOG.md 

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

    nf-core pipelines bump-version 3.16.0dev
    @maxulysse
    maxulysse committed Sep 17, 2024
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Commits on Sep 19, 2024

  1. Merge conflcits

    @egreenberg7
    egreenberg7 committed Sep 19, 2024
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  2. Merge branch 'dev' of github.com:egreenberg7/rnaseq into dev

    @egreenberg7
    egreenberg7 committed Sep 19, 2024
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  3. Update hisat2 patch

    @egreenberg7
    egreenberg7 committed Sep 19, 2024
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  4. (Hopefully) final linting fix

    @egreenberg7
    egreenberg7 committed Sep 19, 2024
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