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[skip ci] Dev -> Master for 3.15.0 #1258

Merged
merged 831 commits into from
Sep 5, 2024
Merged

[skip ci] Dev -> Master for 3.15.0 #1258

merged 831 commits into from
Sep 5, 2024
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Jul 3, 2024

  1. add stubs + code polish + Harshil align

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

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

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

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

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

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

  1. Modify FastQC output publishing to comply with the paths in MultiQC c… 

    …onfig.
    @MatthiasZepper
    MatthiasZepper committed Jul 4, 2024
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  2. MultiQC config updates.

    @MatthiasZepper
    MatthiasZepper committed Jul 4, 2024
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  3. Linting.

    @MatthiasZepper
    MatthiasZepper committed Jul 4, 2024
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  4. Use the correct module names to supress the Percent Duplicate column … 

    …in the General Stats table of MultiQC.
    @MatthiasZepper
    MatthiasZepper committed Jul 4, 2024
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  5. Publish logfiles from umi-tools dedup steps.

    @MatthiasZepper
    MatthiasZepper committed Jul 4, 2024
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  6. Modify subworkflow bam_dedup_stats_samtools_umitools to publish dedup… 

    … logs.
    @MatthiasZepper
    MatthiasZepper committed Jul 4, 2024
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  7. Update bam_dedup_stats_samtools_umitools subworkflow and MultiQC module.

    @MatthiasZepper
    MatthiasZepper committed Jul 4, 2024
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  8. Add UMI information for Watchmaker mRNA Library Prep Kit.

    @MatthiasZepper
    MatthiasZepper committed Jul 4, 2024
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  9. Publish the UMI-tools extract logs for MultiQC.

    @MatthiasZepper
    MatthiasZepper committed Jul 4, 2024
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  10. The output channel of fastq_fastqc_umitools_trimgalore/fastp is calle… 

    …d 'umi_log' and not 'log'. The meta.yml is wrong.
    @MatthiasZepper
    MatthiasZepper committed Jul 4, 2024
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  11. Mark FASTQC outputs with suffixes

    @pinin4fjords @MatthiasZepper
    pinin4fjords authored and MatthiasZepper committed Jul 4, 2024
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  12. @aanil (Anandashankar Anil) correctly pointed out that some MultiQC c… 

    …onfiguration parameters used in the config were deprecated.
    @MatthiasZepper
    MatthiasZepper committed Jul 4, 2024
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  13. Linting

    @MatthiasZepper
    MatthiasZepper committed Jul 4, 2024
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  14. Changelog

    @MatthiasZepper
    MatthiasZepper committed Jul 4, 2024
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  15. add plugin

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

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

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

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

    @maxulysse
    maxulysse committed Jul 4, 2024
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  20. 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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  2. Use nf-core/setup-nf-test action for portability

    @adamrtalbot
    adamrtalbot committed Jul 5, 2024
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  3. changelog

    @adamrtalbot
    adamrtalbot 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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  2. Undo changes to modules/nf-core/dupradar/templates/dupradar.r from Ha… 

    …rshil Patel and me, since they should be fixed upstream in the modules directory. Reset state of file to cc1bf2c.
    @MatthiasZepper
    MatthiasZepper committed Jul 9, 2024
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  3. Update Azure Batch guidance 

    Updated Azure Batch guidance to use a machine that would actually work 🤦 .

Do we even need this? Can we just remove this section?
    @adamrtalbot
    adamrtalbot authored Jul 9, 2024
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Commits on Jul 10, 2024

  1. Add suggestions from @MatthiasZepper 

    Co-authored-by: Matthias Zepper <6963520+MatthiasZepper@users.noreply.github.com>
    @lazappi @MatthiasZepper
    lazappi and MatthiasZepper authored Jul 10, 2024
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  2. bump module and temporarily patch for nf-core/modules#5943

    @pinin4fjords
    pinin4fjords committed Jul 10, 2024
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  3. Correct the diff

    @pinin4fjords
    pinin4fjords committed Jul 10, 2024
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  4. Update MultiQC to v1.23

    @MatthiasZepper
    MatthiasZepper committed Jul 10, 2024
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Commits on Jul 11, 2024

  1. Demote titles to return structure to previous

    @pinin4fjords
    pinin4fjords authored Jul 11, 2024
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  2. Update dupradar from modules repo and remove patch.

    @MatthiasZepper
    MatthiasZepper committed Jul 11, 2024
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  3. use seqera containers

    @maxulysse
    maxulysse committed Jul 11, 2024
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  4. Update module for snapshot fix

    @pinin4fjords
    pinin4fjords committed Jul 11, 2024
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  5. Fix prefixes for FASTQC

    @pinin4fjords
    pinin4fjords committed Jul 11, 2024
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Commits on Jul 12, 2024

  1. Merge pull request #1308 from MatthiasZepper/MultiQC_FastQC_bug 

    Various MultiQC issues: FastQC sections for raw and trimmed reads // umi-tools dedup and extraction plots, custom content styling.
    @MatthiasZepper
    MatthiasZepper authored Jul 12, 2024
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  2. Merge branch 'dev' into stubs_everywhere

    @maxulysse
    maxulysse authored Jul 12, 2024
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  3. update all modules/subworkflows + remove tags

    @maxulysse
    maxulysse committed Jul 12, 2024
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  4. Apply a blanket renaming in multiqc to catch inconsistent naming pair… 

    …ed and unpaired
    @pinin4fjords
    pinin4fjords committed Jul 12, 2024
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  5. Switch renaming to exact matches

    @pinin4fjords
    pinin4fjords committed Jul 12, 2024
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  6. update snapshot

    @maxulysse
    maxulysse committed Jul 12, 2024
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  7. Bump multiqc module

    @pinin4fjords
    pinin4fjords committed Jul 12, 2024
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  8. Separate rename patterns for forward and reverse

    @pinin4fjords
    pinin4fjords committed Jul 12, 2024
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  9. update CHANGELOG

    @pinin4fjords
    pinin4fjords committed Jul 12, 2024
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  10. Remove Azure specific guidance 

    No longer necessary.
    @adamrtalbot
    adamrtalbot authored Jul 12, 2024
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  11. Merge branch 'dev' into update-azure-batch-guidance

    @adamrtalbot
    adamrtalbot authored Jul 12, 2024
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  12. Update CHANGELOG.md

    @adamrtalbot
    adamrtalbot authored Jul 12, 2024
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Commits on Jul 15, 2024

  1. simplify logic to generate renaming table

    @pinin4fjords
    pinin4fjords committed Jul 15, 2024
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  2. Merge pull request #1340 from nf-core/update-azure-batch-guidance 

    Update Azure Batch guidance
    @pinin4fjords
    pinin4fjords authored Jul 15, 2024
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  3. Merge branch 'dev' into rename_samples

    @pinin4fjords
    pinin4fjords authored Jul 15, 2024
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  4. Update CHANGELOG

    @MatthiasZepper
    MatthiasZepper committed Jul 15, 2024
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  5. Merge pull request #1314 from lazappi/annotation-documentation 

    Add reference recommendations to usage docs
    @MatthiasZepper
    MatthiasZepper authored Jul 15, 2024
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  6. Make name replacement specific to samples without tech reps

    @pinin4fjords
    pinin4fjords committed Jul 15, 2024
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  7. Merge branch 'rename_samples' of https://github.com/nf-core/rnaseq in… 

    …to rename_samples
    @pinin4fjords
    pinin4fjords committed Jul 15, 2024
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  8. Clarify comment

    @pinin4fjords
    pinin4fjords authored Jul 15, 2024
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  9. Update main.nf

    @pinin4fjords
    pinin4fjords authored Jul 15, 2024
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  10. Update CHANGELOG.md

    @pinin4fjords
    pinin4fjords authored Jul 15, 2024
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  11. Merge pull request #1341 from nf-core/rename_samples 

    Add rename in the MultiQC report for samples without techreps
    @pinin4fjords
    pinin4fjords authored Jul 15, 2024
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  12. Merge branch 'dev' into use_nf_test_action

    @pinin4fjords
    pinin4fjords authored Jul 15, 2024
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  13. Merge pull request #1336 from adamrtalbot/use_nf_test_action 

    Use nf-core/setup-nf-test action for portability
    @pinin4fjords
    pinin4fjords authored Jul 15, 2024
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Commits on Jul 16, 2024

  1. Merge branch 'dev' into stubs_everywhere

    @maxulysse
    maxulysse authored Jul 16, 2024
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  2. Factor out preprocessing logic to nf-core subworkflow

    @pinin4fjords
    pinin4fjords committed Jul 16, 2024
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  3. update changelog

    @pinin4fjords
    pinin4fjords committed Jul 16, 2024
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Commits on Jul 17, 2024

  1. Update RNAseq preprocessing swf

    @pinin4fjords
    pinin4fjords committed Jul 17, 2024
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  2. update modules.json

    @pinin4fjords
    pinin4fjords committed Jul 17, 2024
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  3. fix up ribo db wiring

    @pinin4fjords
    pinin4fjords committed Jul 17, 2024
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  4. Install swf from branch for now

    @pinin4fjords
    pinin4fjords committed Jul 17, 2024
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  5. Fix tests

    @pinin4fjords
    pinin4fjords committed Jul 17, 2024
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  6. Update modules.json

    @pinin4fjords
    pinin4fjords committed Jul 17, 2024
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  7. Move strandedness function testing to swf

    @pinin4fjords
    pinin4fjords committed Jul 17, 2024
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  8. Install from modules master

    @pinin4fjords
    pinin4fjords committed Jul 17, 2024
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  9. Strip preprocessing components relocated to subworkflows

    @pinin4fjords
    pinin4fjords committed Jul 17, 2024
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  10. Merge branch 'factor_out_preprocessing' of https://github.com/nf-core… 

    …/rnaseq into factor_out_preprocessing
    @pinin4fjords
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  11. Merge pull request #1342 from nf-core/factor_out_preprocessing 

    Factor out preprocessing
    @pinin4fjords
    pinin4fjords authored Jul 17, 2024
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Commits on Jul 19, 2024

  1. Fix the new call to preprocessing subworkflow

    @pinin4fjords
    pinin4fjords committed Jul 19, 2024
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  2. Fix the new call to preprocessing subworkflow

    @pinin4fjords
    pinin4fjords committed Jul 19, 2024
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  3. Fix the new call to preprocessing subworkflow

    @pinin4fjords
    pinin4fjords committed Jul 19, 2024
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  4. Merge branch 'fix_preprocessing_call' of github.com:nf-core/rnaseq in… 

    …to fix_preprocessing_call
    @pinin4fjords
    pinin4fjords committed Jul 19, 2024
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  5. Remove print

    @pinin4fjords
    pinin4fjords committed Jul 19, 2024
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  6. update changelog

    @pinin4fjords
    pinin4fjords committed Jul 19, 2024
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  7. Merge pull request #1345 from nf-core/fix_preprocessing_call 

    Fix preprocessing call
    @pinin4fjords
    pinin4fjords authored Jul 19, 2024
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Commits on Jul 22, 2024

  1. Merge branch 'dev' into stubs_everywhere

    @maxulysse
    maxulysse authored 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 Aug 7, 2024

  1. Bump resource bucket for genomecov

    @pinin4fjords
    pinin4fjords committed Aug 7, 2024
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  2. Revert "Bump resource bucket for genomecov" 

    This reverts commit 61def16.
    @pinin4fjords
    pinin4fjords committed Aug 7, 2024
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  3. Update bedtools/genomecov for lower-resource sort

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    pinin4fjords committed Aug 7, 2024
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  4. Update changelog

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  5. Merge pull request #1350 from nf-core/bump_bedtools_mem 

    Reduce resource usage for sort process in bedtools/genomecov
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  6. Try multiqc fixes

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Commits on Aug 8, 2024

  1. Fix rename patterns

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  2. Import tsv func from nf-core subworkflow

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    pinin4fjords committed Aug 8, 2024
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  3. Better define ordering

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

    …ting
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Commits on Aug 9, 2024

  1. Fix up methods and versions passed to MultiQC

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

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  3. Temp fix pending suworkflow update

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  4. update subworkflow from nf-core

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  5. update changelog

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

  1. correct conditional for salmon indexing in proprocessing workflow

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  2. Update CHANGELOG.md

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Commits on Aug 16, 2024

  1. Merge pull request #1353 from nf-core/prepro_indexing_fix 

    Correct conditional for salmon indexing in preprocessing workflow
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  2. Merge branch 'dev' into stubs_everywhere

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

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

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  5. Merge branch 'dev' into harmonize_new_for_multiqc

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    pinin4fjords committed Aug 16, 2024
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Commits on Aug 19, 2024

  1. Update multiqc for prefix usage

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  2. tiny updates on subway map

    @maxulysse
    maxulysse committed Aug 19, 2024
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  3. realign

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

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  5. update CHANGELOG

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    maxulysse committed Aug 19, 2024
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  6. Update CHANGELOG.md

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Commits on Aug 20, 2024

  1. Bump multiqc

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

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

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

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

    Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
    @pinin4fjords @adamrtalbot
    pinin4fjords and adamrtalbot authored Aug 20, 2024
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  6. Merge pull request #1352 from nf-core/harmonize_new_for_multiqc 

    Assorted fixes to MultiQC usage
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  7. Merge branch 'dev' into stubs_everywhere

    @maxulysse
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  8. clean up stub tests

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

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

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  11. Merge pull request #1357 from nf-core/fix_anchor_issue 

    Work around anchor issue in multiqc
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  12. Merge branch 'dev' into stubs_everywhere

    @maxulysse
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  13. update CHANGELOG

    @maxulysse
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  14. Animate subway map

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

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

  1. update snapshot

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  2. Merge pull request #1335 from maxulysse/stubs_everywhere 

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

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

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    pinin4fjords authored Aug 21, 2024
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  5. use permalink

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    pinin4fjords authored Aug 21, 2024
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  6. Same for minimal tests

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  7. Update CHANGELOG.md

    @pinin4fjords
    pinin4fjords authored 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
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  10. Fix input

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

    Update test_full.config to restore a static URI for megatests
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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

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

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

    @maxulysse
    maxulysse authored 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 #1359 from nf-core/revert_multiqc_workaround 

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

    @maxulysse
    maxulysse authored 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 #1362 from nf-core/multiqc_test_config 

    Move multiqc module prefix for nf-test to module
    @maxulysse
    maxulysse authored 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 authored 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
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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 authored 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
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  26. typo

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

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  28. text to path

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Commits on Aug 23, 2024

  1. update snapshots

    @maxulysse
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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

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    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

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  2. Merge pull request #1361 from maxulysse/animate_subway 

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

    @maxulysse
    maxulysse authored 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 #1360 from maxulysse/moar_snapshots 

    Snapshot all files (content or file name when not stable)
    @maxulysse
    maxulysse authored 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 #1363 from maxulysse/last_fix_before_3-15 

    Fixing failing tests and updating modules once more
    @maxulysse
    maxulysse authored 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 authored Sep 3, 2024
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  2. Update docs/output.md

    @pinin4fjords
    pinin4fjords authored 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 authored Sep 3, 2024
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  4. Update CHANGELOG.md

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

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

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

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

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

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

    Clarify docs on different tximport count files
    @pinin4fjords
    pinin4fjords authored 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 <max.u.garcia@gmail.com>
    @pinin4fjords @maxulysse
    pinin4fjords and maxulysse authored 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 #1370 from nf-core/prerelease_3.15.0_fixes 

    Bump versions for 3.15.0
    @pinin4fjords
    pinin4fjords authored 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 #1371 from nf-core/maxime_changelog_changes 

    Apply Maxime's changelog edits
    @pinin4fjords
    pinin4fjords authored 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 #1372 from nf-core/bump_tximport_gene_names 

    Bump tximeta/tximport for gene table row names fix
    @pinin4fjords
    pinin4fjords authored Sep 4, 2024
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