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Patch release: 1.1.6 #469

Merged
merged 65 commits into from
Apr 16, 2024
Merged

Patch release: 1.1.6 #469

merged 65 commits into from
Apr 16, 2024

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 #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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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 28, 2024

  1. make full-pathed SVGs rather than text versions of the logos

    @jfy133
    jfy133 committed Feb 28, 2024
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  2. Include font-fullpath metromap

    @jfy133
    jfy133 committed Feb 28, 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 #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 branch 'dev' of github.com:nf-core/taxprofiler into logo-fix

    @jfy133
    jfy133 committed Mar 14, 2024
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  2. Merge pull request #453 from nf-core/logo-fix 

    Logo fix
    @jfy133
    jfy133 authored Mar 14, 2024
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Commits on Mar 18, 2024

  1. correct nanopore and fasta input channel

    @LilyAnderssonLee
    LilyAnderssonLee committed Mar 18, 2024
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  2. Merge pull request #459 from LilyAnderssonLee/fix-validation-dev 

    correct nanopore and fasta input channel - branch "dev"
    @maxulysse
    maxulysse authored Mar 18, 2024
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Commits on Mar 21, 2024

  1. Try adding nextflow strict

    @jfy133
    jfy133 committed Mar 21, 2024
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  2. Start fixing untar MALT db error

    @jfy133
    jfy133 committed Mar 21, 2024
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  3. update nf-validation and turn off kaiju2krona output

    @LilyAnderssonLee
    LilyAnderssonLee committed Mar 21, 2024
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  4. Optimise database untarring and prevent publishing clashses

    @jfy133
    jfy133 committed Mar 21, 2024
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  5. Update changelog

    @jfy133
    jfy133 committed Mar 21, 2024
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  6. Merge pull request #463 from LilyAnderssonLee/update-validation 

    Update nf-validation and turn off kaiju2krona output
    @LilyAnderssonLee
    LilyAnderssonLee authored Mar 21, 2024
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  7. Update changelog

    @jfy133
    jfy133 committed Mar 21, 2024
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  8. Add nf-validation specific parameter to ignore list

    @jfy133
    jfy133 committed Mar 21, 2024
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Commits on Mar 22, 2024

  1. Remove a debugging dump

    @jfy133
    jfy133 committed Mar 22, 2024
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  2. Remove final dump

    @jfy133
    jfy133 committed Mar 22, 2024
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  3. Actually remove it

    @jfy133
    jfy133 committed Mar 22, 2024
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Commits on Mar 28, 2024

  1. Fix occasional split errors, due to db_params replacement not actuall… 

    …y being assigned to a channel, ensure new metamap made on db_param cleanup
    @jfy133
    jfy133 committed Mar 28, 2024
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  2. Update workflows/taxprofiler.nf 

    Co-authored-by: Moritz E. Beber <[email protected]>
    @jfy133 @Midnighter
    jfy133 and Midnighter authored Mar 28, 2024
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Commits on Apr 4, 2024

  1. Add option to save uncompressed databases, turn 

    off Kraken2 to krona conversion output file
publishing
    @jfy133
    jfy133 committed Apr 4, 2024
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  2. Apply suggestions from code review

    @jfy133
    jfy133 authored Apr 4, 2024
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  3. [automated] Fix code linting

    @nf-core-bot
    nf-core-bot committed Apr 4, 2024
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  4. Update CHANGELOG.md 

    Co-authored-by: Lili Andersson-Li <[email protected]>
    @jfy133 @LilyAnderssonLee
    jfy133 and LilyAnderssonLee authored Apr 4, 2024
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  5. Update nextflow_schema.json 

    Co-authored-by: Lili Andersson-Li <[email protected]>
    @jfy133 @LilyAnderssonLee
    jfy133 and LilyAnderssonLee authored Apr 4, 2024
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  6. Merge pull request #461 from nf-core/nextflow-enable-strict 

    Try adding nextflow strict
    @jfy133
    jfy133 authored Apr 4, 2024
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Commits on Apr 6, 2024

  1. chore: avoid mOTUs download progress report

    @Midnighter
    Midnighter committed Apr 6, 2024
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  2. fix: transform channels to combine on DB name 

    Change wording of function and parameters description.
    @Midnighter
    Midnighter committed Apr 6, 2024
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  3. refactor: extraction function to group profiles

    @Midnighter
    Midnighter committed Apr 6, 2024
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  4. docs: add changelog entry

    @Midnighter
    Midnighter committed Apr 6, 2024
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  5. fix: correct file name for combined kraken2 reports

    @Midnighter
    Midnighter committed Apr 6, 2024
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Commits on Apr 7, 2024

  1. chore: remove channel dumps used for debugging 

    Co-authored-by: Lili Andersson-Li <[email protected]>
    @Midnighter @LilyAnderssonLee
    Midnighter and LilyAnderssonLee authored Apr 7, 2024
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  2. Merge pull request #464 from nf-core/fix-combine 

    Fix combine
    @Midnighter
    Midnighter authored Apr 7, 2024
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Commits on Apr 11, 2024

  1. bump the version

    @LilyAnderssonLee
    LilyAnderssonLee committed Apr 11, 2024
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  2. Merge pull request #468 from LilyAnderssonLee/bump_version 

    bump the version
    @LilyAnderssonLee
    LilyAnderssonLee authored Apr 11, 2024
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Commits on Apr 12, 2024

  1. update download-pipeline.yml

    @LilyAnderssonLee
    LilyAnderssonLee committed Apr 12, 2024
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  2. update download-pipeline.yml

    @LilyAnderssonLee
    LilyAnderssonLee committed Apr 12, 2024
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  3. Merge pull request #470 from LilyAnderssonLee/fix-download-pipeline 

    Fix download pipeline workflow
    @LilyAnderssonLee
    LilyAnderssonLee authored Apr 12, 2024
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  4. manully define stub run branch is master

    @LilyAnderssonLee
    LilyAnderssonLee committed Apr 12, 2024
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  5. update changelog and remove disk clean in download_pipeline.yml

    @LilyAnderssonLee
    LilyAnderssonLee committed Apr 12, 2024
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  6. Update download_pipeline.yml

    @LilyAnderssonLee
    LilyAnderssonLee authored Apr 12, 2024
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Commits on Apr 16, 2024

  1. remove stub run in download pipeline

    @LilyAnderssonLee
    LilyAnderssonLee committed Apr 16, 2024
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  2. Merge pull request #471 from LilyAnderssonLee/download-pipeline-bug 

    Remove stub run in download_pipeline.yml
    @jfy133
    jfy133 authored Apr 16, 2024
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