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Release 3.1.0 #679

Merged
merged 36 commits into from
Oct 4, 2024
Merged

Release 3.1.0 #679

merged 36 commits into from
Oct 4, 2024

Commits on Aug 27, 2024

  1. Bump versions

    @jfy133
    jfy133 committed Aug 27, 2024
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  2. Merge pull request #658 from nf-core/postrelease-bump 

    Bump versions post release
    @jfy133
    jfy133 authored Aug 27, 2024
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Commits on Sep 8, 2024

  1. Update GTDBTk to v2.4.0

    @dialvarezs
    dialvarezs committed Sep 8, 2024
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  2. Changelog

    @dialvarezs
    dialvarezs committed Sep 8, 2024
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  3. Prettier

    @dialvarezs
    dialvarezs committed Sep 8, 2024
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Commits on Sep 9, 2024

  1. Bump GTDB release version, better changelog

    @jfy133
    jfy133 committed Sep 9, 2024
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  2. Add support for pre-supplying bowtie2 host index

    @jfy133
    jfy133 committed Sep 9, 2024
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Commits on Sep 10, 2024

  1. Merge pull request #664 from dialvarezs/dev-gtdbtk 

    Bump GTDBTk to v2.4.0
    @jfy133
    jfy133 authored Sep 10, 2024
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  2. Merge pull request #665 from nf-core/bowtie2-index 

    Add support for pre-supplying host reference bowtie2 index
    @jfy133
    jfy133 authored Sep 10, 2024
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Commits on Sep 11, 2024

  1. Improve condition so SPLIT_FASTQ skipped if only concoct selected as … 

    …binner
    @jfy133
    jfy133 committed Sep 11, 2024
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Commits on Sep 12, 2024

  1. Update subworkflows/local/binning.nf

    @jfy133
    jfy133 authored Sep 12, 2024
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  2. Update subworkflows/local/binning.nf

    @jfy133
    jfy133 authored Sep 12, 2024
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  3. Merge pull request #667 from nf-core/concoct-only-fix 

    Improve condition so SPLIT_FASTQ skipped if only concoct selected as …
    @jfy133
    jfy133 authored Sep 12, 2024
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Commits on Sep 13, 2024

  1. Fix module failure when no bins

    @jfy133
    jfy133 committed Sep 13, 2024
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Commits on Sep 16, 2024

  1. Address comments via ofifical module update

    @jfy133
    jfy133 committed Sep 16, 2024
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  2. Merge pull request #669 from nf-core/fix-gtdbtk 

    Fix gtdbtk failing if nothing in align
    @dialvarezs
    dialvarezs authored Sep 16, 2024
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Commits on Sep 18, 2024

  1. Utilise missing GTDBK parameters, rename pplacer scratch due to subop… 

    …timal default
    @jfy133
    jfy133 committed Sep 18, 2024
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  2. Update CHANGELOG

    @jfy133
    jfy133 committed Sep 18, 2024
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  3. Merge branch 'dev' into gtdbtk-missing-params

    @jfy133
    jfy133 authored Sep 18, 2024
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  4. Specify they are parameters

    @jfy133
    jfy133 committed Sep 18, 2024
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  5. Merge branch 'gtdbtk-missing-params' of github.com:nf-core/mag into g… 

    …tdbtk-missing-params
    @jfy133
    jfy133 committed Sep 18, 2024
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Commits on Sep 20, 2024

  1. Typo fixes after review from @harper357

    @jfy133
    jfy133 committed Sep 20, 2024
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  2. REname scratchoff to more intiuitive name to match behaviour

    @jfy133
    jfy133 committed Sep 20, 2024
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  3. Fix missing GTDBTk files in outdir

    @jfy133
    jfy133 committed Sep 20, 2024
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  4. Update CHANGELOG.md 

    Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
    @jfy133 @d4straub
    jfy133 and d4straub authored Sep 20, 2024
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  5. Merge pull request #673 from nf-core/missing-gtdbtk-files 

    Fix missing GTDBTk files in outdir
    @jfy133
    jfy133 authored Sep 20, 2024
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Commits on Sep 23, 2024

  1. Add exit code 12 to spades(hybrid), and standardise errorStrategy format

    @jfy133
    jfy133 committed Sep 23, 2024
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  2. Merge branch 'dev' into gtdbtk-missing-params

    @jfy133
    jfy133 authored Sep 23, 2024
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  3. Merge pull request #671 from nf-core/gtdbtk-missing-params 

    Re-add unused GTDBTK parameters
    @jfy133
    jfy133 authored Sep 23, 2024
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Commits on Sep 24, 2024

  1. Apply suggestions from code review 

    Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
    @jfy133 @d4straub
    jfy133 and d4straub authored Sep 24, 2024
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  2. Merge pull request #676 from nf-core/spades-ec-12 

    Add exit code 12 to SPAdes and standardise custom errorStragety formats
    @jfy133
    jfy133 authored Sep 24, 2024
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Commits on Oct 2, 2024

  1. Bump version for release

    @jfy133
    jfy133 committed Oct 2, 2024
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  2. Harshil align

    @jfy133
    jfy133 committed Oct 2, 2024
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  3. Merge pull request #678 from nf-core/release-dump 

    Release version bump for 3.1
    @jfy133
    jfy133 authored Oct 2, 2024
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Commits on Oct 3, 2024

  1. Apply suggestions from code review 

    Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
    @jfy133 @mashehu
    jfy133 and mashehu authored Oct 3, 2024
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  2. Update CHANGELOG.md

    @jfy133
    jfy133 authored Oct 3, 2024
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