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Correcting the NANOPORE and FASTA reads channel #457

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wants to merge 48 commits into from
Closed

Correcting the NANOPORE and FASTA reads channel #457

wants to merge 48 commits into from

Commits on Nov 9, 2023

  1. Install module

    @jfy133
    jfy133 committed Nov 9, 2023
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Commits on Nov 10, 2023

  1. Merge pull request nf-core#416 from nf-core/dev 

    Sync with dev
    @jfy133
    jfy133 authored Nov 10, 2023
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  2. Add get it working, add to tests, update docs/images/citations

    @jfy133
    jfy133 committed Nov 10, 2023
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Commits on Nov 13, 2023

  1. Fix groovy semantic errors

    @jfy133
    jfy133 committed Nov 13, 2023
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  2. update gitignore to ignore nf-test

    @jfy133
    jfy133 committed Nov 13, 2023
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  3. Revert "update gitignore to ignore nf-test" 

    This reverts commit 1a37251.
    @jfy133
    jfy133 committed Nov 13, 2023
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Commits on Nov 15, 2023

  1. Fix nonpareil args across all tests

    @jfy133
    jfy133 committed Nov 15, 2023
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Commits on Nov 30, 2023

  1. Add nonpareil

    @jfy133
    jfy133 committed Nov 30, 2023
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  2. Minor linting

    @jfy133
    jfy133 committed Nov 30, 2023
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  3. Fix channel emission

    @jfy133
    jfy133 committed Nov 30, 2023
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  4. Fix module linting

    @jfy133
    jfy133 committed Nov 30, 2023
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  5. Add nonpareil to valid MultiQC entries

    @jfy133
    jfy133 committed Nov 30, 2023
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  6. Final linting

    @jfy133
    jfy133 authored Nov 30, 2023
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  7. [automated] Fix linting with Prettier

    @nf-core-bot
    nf-core-bot committed Nov 30, 2023
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  8. Apply suggestions from code review 

    Co-authored-by: Lili Andersson-Li <[email protected]>
    @jfy133 @LilyAnderssonLee
    jfy133 and LilyAnderssonLee authored Nov 30, 2023
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  9. Merge pull request nf-core#417 from nf-core/add-nonpareil 

    Add nonpareil
    @jfy133
    jfy133 authored Nov 30, 2023
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Commits on Jan 12, 2024

  1. Merge branch 'dev' into bouncy-basenji

    @jfy133
    jfy133 committed Jan 12, 2024
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Commits on Jan 25, 2024

  1. Merge dev into bouncy-basenji

    @sofstam
    sofstam committed Jan 25, 2024
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  2. Fix prettier

    @jfy133
    jfy133 committed Jan 25, 2024
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  3. Remove merge marker

    @jfy133
    jfy133 committed Jan 25, 2024
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Commits on Feb 8, 2024

  1. Apply review suggestions

    @sofstam
    sofstam committed Feb 8, 2024
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  2. Merge branch 'nf-core:dev' into dev

    @sofstam
    sofstam authored Feb 8, 2024
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  3. Bump to new dev version

    @sofstam
    sofstam committed Feb 8, 2024
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  4. Prettier

    @sofstam
    sofstam committed Feb 8, 2024
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  5. Update CHANGELOG.md 

    Co-authored-by: James A. Fellows Yates <[email protected]>
    @sofstam @jfy133
    sofstam and jfy133 authored Feb 8, 2024
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  6. Merge pull request nf-core#447 from genomic-medicine-sweden/bump_version 

    Bump up the pipeline version number in the dev branch
    @sofstam
    sofstam authored Feb 8, 2024
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  7. Merge branch 'bouncy-basenji' into fix-merge-conflict

    @jfy133
    jfy133 authored Feb 8, 2024
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  8. Merge pull request nf-core#448 from nf-core/fix-merge-conflict 

    Dev to bouncy-basenji
    @jfy133
    jfy133 authored Feb 8, 2024
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Commits on Feb 20, 2024

  1. Template update for nf-core/tools version 2.13

    @nf-core-bot
    nf-core-bot committed Feb 20, 2024
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Commits on Feb 29, 2024

  1. Template update for nf-core/tools version 2.13.1

    @nf-core-bot
    nf-core-bot committed Feb 29, 2024
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Commits on Mar 1, 2024

  1. update the template and add nf-validation

    @LilyAnderssonLee
    LilyAnderssonLee committed Mar 1, 2024
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  2. remove custom_dumpsoftwareversions

    @LilyAnderssonLee
    LilyAnderssonLee committed Mar 1, 2024
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  3. Update .github/workflows/ci.yml 

    Co-authored-by: Nicolas Vannieuwkerke <[email protected]>
    @LilyAnderssonLee @nvnieuwk
    LilyAnderssonLee and nvnieuwk authored Mar 1, 2024
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  4. Update ci.yml

    @sofstam
    sofstam authored Mar 1, 2024
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Commits on Mar 4, 2024

  1. update error message in schema_databases.json

    @LilyAnderssonLee
    LilyAnderssonLee committed Mar 4, 2024
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  2. Update the db_path format definition to include both options for file… 

    … path and directory
    @LilyAnderssonLee
    LilyAnderssonLee committed Mar 4, 2024
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Commits on Mar 5, 2024

  1. Update main.nf 

    Co-authored-by: Matthias Hörtenhuber <[email protected]>
    @LilyAnderssonLee @mashehu
    LilyAnderssonLee and mashehu authored Mar 5, 2024
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  2. Update assets/schema_database.json 

    Co-authored-by: Matthias Hörtenhuber <[email protected]>
    @LilyAnderssonLee @mashehu
    LilyAnderssonLee and mashehu authored Mar 5, 2024
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  3. Update assets/schema_database.json 

    Co-authored-by: Matthias Hörtenhuber <[email protected]>
    @LilyAnderssonLee @mashehu
    LilyAnderssonLee and mashehu authored Mar 5, 2024
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  4. Update assets/schema_database.json 

    Co-authored-by: Matthias Hörtenhuber <[email protected]>
    @LilyAnderssonLee @mashehu
    LilyAnderssonLee and mashehu authored Mar 5, 2024
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  5. update db_params in schema_databases.json

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

  1. Update taxprofiler.nf 

    remove commented code about unique db_name check
    @LilyAnderssonLee
    LilyAnderssonLee authored Mar 6, 2024
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  2. Update taxprofiler.nf 

    Replace the db_params:null into empty string "".
    @LilyAnderssonLee
    LilyAnderssonLee authored Mar 6, 2024
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  3. Update taxprofiler.nf 

    Add meta.single_end to ch_input.nanopore channel
    @LilyAnderssonLee
    LilyAnderssonLee authored Mar 6, 2024
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  4. Merge pull request nf-core#454 from nf-core/nf-core-template-merge-2.… 

    …13.1

Important! Template update for nf-core/tools v2.13.1
    @LilyAnderssonLee
    LilyAnderssonLee authored Mar 6, 2024
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Commits on Mar 14, 2024

  1. Merge dev into bouncy-basenji

    @LilyAnderssonLee
    LilyAnderssonLee committed Mar 14, 2024
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Commits on Mar 15, 2024

  1. Merge pull request nf-core#455 from LilyAnderssonLee/bouncy-basenji 

    Merge dev into bouncy-basenji
    @LilyAnderssonLee
    LilyAnderssonLee authored Mar 15, 2024
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Commits on Mar 18, 2024

  1. update the nanopore and fasta input channel

    @LilyAnderssonLee
    LilyAnderssonLee committed Mar 18, 2024
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