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Dev -> Master for 3.12.0 release #1040

Merged
merged 50 commits into from
Jun 2, 2023
Merged

Dev -> Master for 3.12.0 release #1040

merged 50 commits into from
Jun 2, 2023

Commits on Apr 25, 2023

  1. Bump pipeline version to 3.12.0dev

    @drpatelh
    drpatelh committed Apr 25, 2023
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  2. Merge pull request #1012 from drpatelh/updates 

    Bump pipeline version to 3.12.0dev
    @maxulysse
    maxulysse authored Apr 25, 2023
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Commits on Apr 28, 2023

  1. Template update for nf-core/tools version 2.8

    @nf-core-bot
    nf-core-bot committed Apr 28, 2023
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Commits on May 6, 2023

  1. Fix merge conflicts

    @drpatelh
    drpatelh committed May 6, 2023
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  2. Update all nf-core modules and subworkflows

    @drpatelh
    drpatelh committed May 6, 2023
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  3. Update all local modules

    @drpatelh
    drpatelh committed May 6, 2023
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  4. Update CHANGELOG

    @drpatelh
    drpatelh committed May 6, 2023
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  5. Update usage docs

    @drpatelh
    drpatelh committed May 6, 2023
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Commits on May 7, 2023

  1. Fix alignment in nextflow.config

    @drpatelh
    drpatelh committed May 7, 2023
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Commits on May 8, 2023

  1. Remove quay.io prefix from mulled containers

    @drpatelh
    drpatelh committed May 8, 2023
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Commits on May 9, 2023

  1. Update usage docs

    @drpatelh
    drpatelh committed May 9, 2023
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  2. Merge pull request #1016 from nf-core/nf-core-template-merge-2.8 

    Important! Template update for nf-core/tools v2.8
    @drpatelh
    drpatelh authored May 9, 2023
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Commits on May 11, 2023

  1. Set a default docker registry outside of profile scope. 

    The `docker.registry` configuration should always be set, as running
on cloud executors will need to pull docker images but will not
necessarily use the `docker` profile.
    @robsyme
    robsyme committed May 11, 2023
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  2. Update nextflow.config

    @maxulysse
    maxulysse authored May 11, 2023
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  3. Update nextflow.config 

    restore process.shell declaration
    @maxulysse
    maxulysse authored May 11, 2023
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  4. Update README.md 

    Corrected spelling of name "Edmund Miller".
    @Ghepardo
    Ghepardo authored May 11, 2023
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  5. Merge pull request #1021 from nf-core/docker-registry-config-move 

    Set a default docker registry outside of profile scope.
    @drpatelh
    drpatelh authored May 11, 2023
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  6. Merge pull request #1023 from Ghepardo/patch-1 

    Update README.md
    @drpatelh
    drpatelh authored May 11, 2023
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Commits on May 14, 2023

  1. Add public_aws_ecr.config and use in CI tests

    @drpatelh
    drpatelh committed May 14, 2023
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  2. Update CHANGELOG

    @drpatelh
    drpatelh committed May 14, 2023
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  3. Fix ECLint

    @drpatelh
    drpatelh committed May 14, 2023
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Commits on May 15, 2023

  1. PROFILES: test -> test_cache + restore test

    @maxulysse
    maxulysse committed May 15, 2023
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  2. Merge pull request #1025 from drpatelh/updates 

    Add public_aws_ecr.config and use in CI tests
    @drpatelh
    drpatelh authored May 15, 2023
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  3. actually swap the files

    @maxulysse
    maxulysse committed May 15, 2023
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  4. spacing

    @maxulysse
    maxulysse committed May 15, 2023
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  5. Merge branch 'dev' into profile_test_data_base

    @maxulysse
    maxulysse authored May 15, 2023
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Commits on May 23, 2023

  1. Update conf/test.config 

    Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
    @maxulysse @drpatelh
    maxulysse and drpatelh authored May 23, 2023
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Commits on May 24, 2023

  1. Fix for public_aws_ecr profile that didn't match modules sometimes

    @adamrtalbot
    adamrtalbot committed May 24, 2023
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Commits on May 25, 2023

  1. Merge pull request #1031 from nf-core/public_aws_ecr_profile_fix 

    Fix for public_aws_ecr profile that didn't match modules sometimes
    @drpatelh
    drpatelh authored May 25, 2023
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  2. Merge pull request #1026 from maxulysse/profile_test_data_base 

    PROFILES: test -> test_cache + restore test
    @drpatelh
    drpatelh authored May 25, 2023
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  3. Update test configs

    @drpatelh
    drpatelh committed May 25, 2023
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Commits on May 30, 2023

  1. Fix #1011

    @drpatelh
    drpatelh committed May 30, 2023
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Commits on May 31, 2023

  1. Update all modules / subworkflows

    @drpatelh
    drpatelh committed May 31, 2023
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  2. Fix RSEM tests

    @drpatelh
    drpatelh committed May 31, 2023
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  3. Add retry strategy to bbmap/bbsplit

    @drpatelh
    drpatelh committed May 31, 2023
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  4. Merge pull request #1036 from drpatelh/updates 

    Fix #1011
    @drpatelh
    drpatelh authored May 31, 2023
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  5. Fix #1018

    @drpatelh
    drpatelh committed May 31, 2023
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  6. Merge pull request #1037 from drpatelh/updates 

    Fix #1018
    @drpatelh
    drpatelh authored May 31, 2023
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Commits on Jun 1, 2023

  1. Update warning when using --additional_fasta to show clarify gene_bed

    @adamrtalbot
    adamrtalbot committed Jun 1, 2023
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  2. changelog

    @adamrtalbot
    adamrtalbot committed Jun 1, 2023
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  3. Update WorkflowRnaseq.groovy

    @drpatelh
    drpatelh authored Jun 1, 2023
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  4. Merge pull request #1038 from adamrtalbot/update_warning_about_additi… 

    …onal_fasta

Update warning about additional_fasta and gene BED
    @drpatelh
    drpatelh authored Jun 1, 2023
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  5. Bump pipeline version to 3.12.0

    @drpatelh
    drpatelh committed Jun 1, 2023
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  6. Be more explicit with --skip_pseudo_aligner logic

    @drpatelh
    drpatelh committed Jun 1, 2023
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  7. Update CHANGELOG

    @drpatelh
    drpatelh committed Jun 1, 2023
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  8. Merge pull request #1039 from drpatelh/updates 

    Bump pipeline version to 3.12.0
    @drpatelh
    drpatelh authored Jun 1, 2023
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  9. Update public_aws_ecr.config

    @drpatelh
    drpatelh authored Jun 1, 2023
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Commits on Jun 2, 2023

  1. revert samtools_sort to no memory assignement

    @maxulysse
    maxulysse committed Jun 2, 2023
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  2. update CHANGELOG

    @maxulysse
    maxulysse committed Jun 2, 2023
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  3. Merge pull request #1042 from maxulysse/samtools_sort 

    FIX: remove mem assignement for SAMTOOLS_SORT
    @drpatelh
    drpatelh authored Jun 2, 2023
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