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Release candidate 1.4.0 #160

Merged
merged 69 commits into from
Dec 14, 2023
Merged

Release candidate 1.4.0 #160

merged 69 commits into from
Dec 14, 2023

Commits on Jun 5, 2023

  1. Merge branch 'master' of github.com:adamrtalbot/demultiplex

    @adamrtalbot
    adamrtalbot committed Jun 5, 2023
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  2. Merge branch 'master' of github.com:nf-core/demultiplex

    @adamrtalbot
    adamrtalbot committed Jun 5, 2023
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Commits on Jun 8, 2023

  1. Add singularity.registry = 'quay.io' and bump NF version to 23.04.0

    @drpatelh
    drpatelh committed Jun 8, 2023
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  2. Update CHANGELOG

    @drpatelh
    drpatelh committed Jun 8, 2023
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  3. Fix nf-core lint

    @drpatelh
    drpatelh committed Jun 8, 2023
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  4. Fix Prettier

    @drpatelh
    drpatelh committed Jun 8, 2023
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Commits on Jun 14, 2023

  1. Merge pull request #127 from drpatelh/quay.io 

    Add singularity.registry = 'quay.io' and bump NF version to 23.04.0
    @maxulysse
    maxulysse authored Jun 14, 2023
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Commits on Jun 15, 2023

  1. reorganize tests

    @sateeshperi
    sateeshperi committed Jun 15, 2023
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  2. update ci with skip condition for dev

    @sateeshperi
    sateeshperi committed Jun 15, 2023
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  3. fix failing bclconvert test and snap

    @sateeshperi
    sateeshperi committed Jun 15, 2023
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  4. Remove un-necessary registry declarations

    @sateeshperi
    sateeshperi committed Jun 15, 2023
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  5. Merge pull request #129 from nf-core/fix/ci-nf-tests 

    Fix/ci nf tests & Remove un-necessary registry declarations
    @maxulysse
    maxulysse authored Jun 15, 2023
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Commits on Jun 19, 2023

  1. Merge branch 'nf-core:dev' into dev

    @adamrtalbot
    adamrtalbot authored Jun 19, 2023
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  2. Remove public_aws_ecr profile

    @adamrtalbot
    adamrtalbot committed Jun 19, 2023
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Commits on Jun 20, 2023

  1. Update CHANGELOG.md

    @adamrtalbot
    adamrtalbot authored Jun 20, 2023
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  2. Merge pull request #130 from adamrtalbot/remove_aws_ecr_public_profile 

    Remove_aws_ecr_public_profile
    @edmundmiller
    edmundmiller authored Jun 20, 2023
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Commits on Jun 30, 2023

  1. Template update for nf-core/tools version 2.9

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    nf-core-bot committed Jun 30, 2023
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Commits on Aug 22, 2023

  1. Merge branch 'dev' into nf-core-template-merge-2.9

    @edmundmiller
    edmundmiller committed Aug 22, 2023
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  2. fixup! Merge branch 'dev' into nf-core-template-merge-2.9

    @edmundmiller
    edmundmiller committed Aug 22, 2023
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  3. fix: Update input schema 

    Need to work out the required part. I wonder if we can have different
schemas depending on the demultiplexer.

#138
    @edmundmiller
    edmundmiller committed Aug 22, 2023
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  4. chore: Fix test name typo

    @edmundmiller
    edmundmiller committed Aug 22, 2023
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  5. chore: Bump bases2fastq snapshot

    @edmundmiller
    edmundmiller committed Aug 22, 2023
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  6. test: Remove multiqc result file 

    #64 (comment)
    @edmundmiller
    edmundmiller committed Aug 22, 2023
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Commits on Aug 23, 2023

  1. Make it possible to skip multiqc with --skip_tools

    @Aratz
    Aratz committed Aug 23, 2023
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  2. chore: Fix merge error with fastqc 

    Co-authored-by: matthdsm <[email protected]>
    @edmundmiller @matthdsm
    edmundmiller and matthdsm committed Aug 23, 2023
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  3. fix: Remove fasta check all together 

    Co-authored-by: maxulysse <[email protected]>
    @edmundmiller @maxulysse
    edmundmiller and maxulysse committed Aug 23, 2023
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Commits on Aug 24, 2023

  1. Check multiqc report exists in other tests

    @Aratz
    Aratz committed Aug 24, 2023
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  2. Fix old test 

    As seen in `workflows/demultiplex.nf`, when neither trimming nor fastq
are skipped, md5 sums will only be generated for fastp files.
    @Aratz
    Aratz committed Aug 24, 2023
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  3. Add test to check MultiQC can be skipped

    @Aratz
    Aratz committed Aug 24, 2023
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  4. Update snapshot

    @Aratz
    Aratz committed Aug 24, 2023
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  5. Add description in schema for skip_tools

    @Aratz
    Aratz committed Aug 24, 2023
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  6. Fix error raising

    @Aratz
    Aratz committed Aug 24, 2023
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  7. Add contribution to changelog

    @Aratz
    Aratz committed Aug 24, 2023
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  8. Fix tests

    @Aratz
    Aratz committed Aug 24, 2023
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  9. Merge pull request #132 from nf-core/nf-core-template-merge-2.9 

    Important! Template update for nf-core/tools v2.9
    @edmundmiller
    edmundmiller authored Aug 24, 2023
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Commits on Aug 26, 2023

  1. Merge branch 'dev' into dev

    @edmundmiller
    edmundmiller authored Aug 26, 2023
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  2. Merge pull request #140 from Aratz/dev 

    Make it possible to skip MultiQC
    @edmundmiller
    edmundmiller authored Aug 26, 2023
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Commits on Sep 25, 2023

  1. Template update for nf-core/tools version 2.10

    @nf-core-bot
    nf-core-bot committed Sep 25, 2023
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Commits on Oct 17, 2023

  1. Merge remote-tracking branch 'origin/dev' into nf-core-template-merge… 

    …-2.10
    @Aratz
    Aratz committed Oct 17, 2023
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  2. update modules

    @Aratz
    Aratz committed Oct 17, 2023
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  3. Update test snapshots

    @Aratz
    Aratz committed Oct 17, 2023
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  4. docs: Clean up badges

    @edmundmiller
    edmundmiller committed Oct 17, 2023
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  5. chore: Update CHANGELOG

    @edmundmiller
    edmundmiller committed Oct 17, 2023
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  6. ci: Bump nf-test version

    @edmundmiller
    edmundmiller committed Oct 17, 2023
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  7. Merge pull request #141 from nf-core/nf-core-template-merge-2.10 

    Important! Template update for nf-core/tools v2.10
    @edmundmiller
    edmundmiller authored Oct 17, 2023
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  8. Remove multiqc channel reset

    @Aratz
    Aratz committed Oct 17, 2023
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  9. Update changelog

    @Aratz
    Aratz committed Oct 17, 2023
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  10. Merge pull request #145 from Aratz/fix_multiqc_report 

    Fix MultiQC report generation
    @Aratz
    Aratz authored Oct 17, 2023
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Commits on Oct 31, 2023

  1. update bclconvert to 4.2.4

    @maxulysse
    maxulysse committed Oct 31, 2023
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  2. update snapshot

    @maxulysse
    maxulysse committed Oct 31, 2023
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  3. update CHANGELOG

    @maxulysse
    maxulysse committed Oct 31, 2023
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Commits on Nov 2, 2023

  1. Merge pull request #152 from maxulysse/bclconvert 

    FEAT: update bclconvert to 4.2.4
    @edmundmiller
    edmundmiller authored Nov 2, 2023
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  2. chore: Update CODEOWNERS to use teams

    @edmundmiller
    edmundmiller committed Nov 2, 2023
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  3. Merge pull request #148 from nf-core/teams 

    Use teams in CODEOWNERS
    @edmundmiller
    edmundmiller authored Nov 2, 2023
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Commits on Dec 11, 2023

  1. Fix bcl2fastq publishdir 

    There should be no space after a comma when using `{xx,yy}` in a glob.

This also fixes the bcl2fastq test snapshot
    @Aratz
    Aratz committed Dec 11, 2023
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  2. Remove RunInfo.xml from publishDir 

    RunInfo.xml is not an output file of bclconvert nor bcl2fastq, it is
generated by the instrument.
    @Aratz
    Aratz committed Dec 11, 2023
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  3. Update nf-test to 0.8.2

    @Aratz
    Aratz committed Dec 11, 2023
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  4. Update CHANGELOG.md

    @Aratz
    Aratz committed Dec 11, 2023
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  5. Merge pull request #157 from Aratz/fix_publishdirs 

    Fix `bcl2fastq` and `bclconvert` publishDir
    @edmundmiller
    edmundmiller authored Dec 11, 2023
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Commits on Dec 12, 2023

  1. Update all modules 

    Fixes #156
    @Aratz
    Aratz committed Dec 12, 2023
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  2. Update changelog

    @Aratz
    Aratz committed Dec 12, 2023
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  3. fix: Set fastqs to publish_dir_mode 

    #154
    @edmundmiller
    edmundmiller committed Dec 12, 2023
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  4. ci: Bump Nextflow version 

    Co-authored-by: aratz <[email protected]>
    @edmundmiller @Aratz
    edmundmiller and Aratz committed Dec 12, 2023
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  5. Merge pull request #158 from Aratz/module_update 

    Update all modules
    @edmundmiller
    edmundmiller authored Dec 12, 2023
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  6. Merge pull request #155 from nf-core/mode 

    Set publish mode for FastQs
    @edmundmiller
    edmundmiller authored Dec 12, 2023
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Commits on Dec 14, 2023

  1. Bump version to 1.4.0 

    Ran `nf-core bump-version 1.4.0`
    @Aratz
    Aratz committed Dec 14, 2023
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  2. Update CHANGELOG.md

    @Aratz
    Aratz committed Dec 14, 2023
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  3. Fix indentation nextflow.config 

    Co-authored-by: Maxime U Garcia <[email protected]>
    @Aratz @maxulysse
    Aratz and maxulysse authored Dec 14, 2023
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  4. Merge pull request #159 from Aratz/dev 

    Pre-release v1.4.0
    @Aratz
    Aratz authored Dec 14, 2023
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