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Add Metaphlan4 profiler #318

Merged
merged 33 commits into from
Jul 17, 2023
Merged

Add Metaphlan4 profiler #318

merged 33 commits into from
Jul 17, 2023

Commits on Jul 7, 2023

  1. Add MetaPhlAn4 citation to CITATIONS.md

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 7, 2023
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  2. Add MetaPhlAn4 to README.md

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 7, 2023
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  3. Add profiler MetaPhlAn4 to modules.config

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 7, 2023
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  4. Add profiler MetaPhlAn4 to conf/test.config

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 7, 2023
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  5. Add profiler MetaPhlAn4 to conf/test_full.config

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 7, 2023
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  6. Add profiler MetaPhlAn4 to conf/test_krakenuniq.config

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 7, 2023
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  7. Add profiler MetaPhlAn4 to conf/test_motus.config

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 7, 2023
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  8. Add profiler MetaPhlAn4 to conf/test_nopreprocessing.coconfig

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 7, 2023
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  9. Add profiler MetaPhlAn4 to conf/test_noprofiling.config

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 7, 2023
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  10. Add profiler MetaPhlAn4 to conf/test_nothing.config

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 7, 2023
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  11. Add profiler MetaPhlAn4 to docs/images/taxprofiler_tube.svg

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 7, 2023
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  12. Add MetaPhlAn4 to docs/output.md, docs/usage.md

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 7, 2023
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  13. Added parameters to nextflow.config

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 7, 2023
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  14. remove the module metaphlan3/metaphlan3

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 7, 2023
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  15. Remove the module metaphlan3/mergemetaphlantables

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 7, 2023
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  16. update the version of module taxpasta/merge, taxpasta/standardise

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 7, 2023
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  17. Added profiler to expected tools in subworkflows/local/db_check.nf

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 7, 2023
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  18. Added profiler to subworkflows/local/profiling.nf

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 7, 2023
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  19. Added profiler to subworkflows/local/standardisation_profiles.nf

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 7, 2023
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  20. update the pipeline schema

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 7, 2023
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  21. install the module metaphlan

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 7, 2023
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  22. nf-core lint fix format .github/CONTRIBUTING.md

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 7, 2023
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  23. nf-core lint fix format

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 7, 2023
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  24. Update into the most recent version on dev

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 7, 2023
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Commits on Jul 10, 2023

  1. Modify nextflow_schema.json

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 10, 2023
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Commits on Jul 13, 2023

  1. comment krakenuniq step ci.yml

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 13, 2023
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  2. Merge branch 'dev' into metaphlan4_profiler

    @jfy133
    jfy133 committed Jul 13, 2023
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  3. Add MetaPhlAn4 to docs/usage.md

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 13, 2023
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  4. Add contribution to the CHANGELOG.md

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 13, 2023
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Commits on Jul 14, 2023

  1. uncomment KrakenUniq in ci.yml

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 14, 2023
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  2. pull the ci.yml from dev branch

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 14, 2023
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Commits on Jul 17, 2023

  1. Merge branch 'dev' into metaphlan4_profiler

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 17, 2023
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  2. Update CHANGELOG.md

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 17, 2023
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