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Update modules #512

Merged
merged 32 commits into from
Sep 9, 2024
Merged

Update modules #512

merged 32 commits into from
Sep 9, 2024

Commits on Jun 20, 2024

  1. Merge pull request nf-core#499 from nf-core/dev 

    1.1.8 Patch Release
    @jfy133
    jfy133 authored Jun 20, 2024
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Commits on Aug 2, 2024

  1. update modules

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 2, 2024
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  2. update ganon malt motus

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 2, 2024
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Commits on Aug 7, 2024

  1. update filtlong,ganon,krakentools

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

  1. update bracken

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 8, 2024
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  2. add diamond warning for paired-end reads

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 8, 2024
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Commits on Aug 9, 2024

  1. update krona,nonpareil and krakentools

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 9, 2024
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  2. update CHANGELOG.md

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 9, 2024
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  3. update megan/rma2info

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 9, 2024
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Commits on Aug 27, 2024

  1. update metaphlan to the lastest

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 27, 2024
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  2. Merge branch 'bouncy-basenji' into update_tools

    @LilyAnderssonLee
    LilyAnderssonLee authored Aug 27, 2024
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Commits on Aug 28, 2024

  1. Update Multiqc to the latest

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 28, 2024
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Commits on Aug 30, 2024

  1. Add nanoq in the multiqc report

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 30, 2024
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Commits on Sep 3, 2024

  1. Fix bug where Nanopore FASTA files would be picked up into the FASTQ … 

    …branch and thus not passed into the right FASTA channels
    @jfy133
    jfy133 committed Sep 3, 2024
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  2. Use Ida's GH handle

    @jfy133
    jfy133 authored Sep 3, 2024
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Commits on Sep 4, 2024

  1. Update CHANGELOG.md 

    Co-authored-by: Lili Andersson-Li <[email protected]>
    @jfy133 @LilyAnderssonLee
    jfy133 and LilyAnderssonLee authored Sep 4, 2024
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  2. Update docs/usage.md

    @jfy133
    jfy133 authored Sep 4, 2024
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  3. Publish the ganon classify log file in the output

    @LilyAnderssonLee
    LilyAnderssonLee committed Sep 4, 2024
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  4. update motus/profile

    @LilyAnderssonLee
    LilyAnderssonLee committed Sep 4, 2024
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  5. update modules, most changes happened in nf-test

    @LilyAnderssonLee
    LilyAnderssonLee committed Sep 4, 2024
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  6. update utils_nextflow_pipeline and utils_nfcore_pipeline

    @LilyAnderssonLee
    LilyAnderssonLee committed Sep 4, 2024
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Commits on Sep 5, 2024

  1. Merge pull request nf-core#518 from nf-core/fix-nanopore-fasta 

    Fix nanopore fasta input being incorrectly channeled
    @LilyAnderssonLee
    LilyAnderssonLee authored Sep 5, 2024
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  2. Merge branch 'nf-core:master' into update_tools

    @LilyAnderssonLee
    LilyAnderssonLee authored Sep 5, 2024
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  3. merge dev to the current branch

    @LilyAnderssonLee
    LilyAnderssonLee committed Sep 5, 2024
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  4. separate fasta into fasta_shrt and fasta_long

    @LilyAnderssonLee
    LilyAnderssonLee committed Sep 5, 2024
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  5. Update changelog

    @LilyAnderssonLee
    LilyAnderssonLee committed Sep 5, 2024
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  6. add nanoq is default option to the usage

    @LilyAnderssonLee
    LilyAnderssonLee committed Sep 5, 2024
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Commits on Sep 6, 2024

  1. unique check for fasta file names

    @LilyAnderssonLee
    LilyAnderssonLee committed Sep 6, 2024
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  2. state that the pipeline is built on nextflow to README.md

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

    Co-authored-by: Sofia Stamouli <[email protected]>
    @LilyAnderssonLee @sofstam
    LilyAnderssonLee and sofstam authored Sep 6, 2024
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  4. Update CHANGELOG.md

    @LilyAnderssonLee
    LilyAnderssonLee authored Sep 6, 2024
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Commits on Sep 7, 2024

  1. update modules

    @LilyAnderssonLee
    LilyAnderssonLee committed Sep 7, 2024
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