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Manual attempt of template sync for 3.0.2 #695

Merged
merged 22 commits into from
Oct 22, 2024
Merged

Manual attempt of template sync for 3.0.2 #695

merged 22 commits into from
Oct 22, 2024

Commits on Oct 8, 2024

  1. Template update for nf-core/tools version 3.0.0

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    nf-core-bot committed Oct 8, 2024
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Commits on Oct 9, 2024

  1. Template update for nf-core/tools version 3.0.1

    @nf-core-bot
    nf-core-bot committed Oct 9, 2024
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Commits on Oct 11, 2024

  1. Template update for nf-core/tools version 3.0.2

    @nf-core-bot
    nf-core-bot committed Oct 11, 2024
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Commits on Oct 16, 2024

  1. Merge branch 'dev' of github.com:nf-core/mag into nf-core-template-me… 

    …rge-3.0.2-manual
    @jfy133
    jfy133 committed Oct 16, 2024
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  2. Remove unused parameters

    @jfy133
    jfy133 committed Oct 16, 2024
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  3. Comment out unusued tempalte parmaeter (renaming), and remove a dupli… 

    …cate entry in schema
    @jfy133
    jfy133 committed Oct 16, 2024
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  4. Fix yaml indentation

    @jfy133
    jfy133 committed Oct 16, 2024
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  5. Remove nonexistant section

    @jfy133
    jfy133 committed Oct 16, 2024
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  6. Remove unused aprameter

    @jfy133
    jfy133 committed Oct 16, 2024
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Commits on Oct 17, 2024

  1. Remove reference to max_* params and fix input schema

    @jfy133
    jfy133 committed Oct 17, 2024
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  2. Remoce references to check_max()

    @jfy133
    jfy133 committed Oct 17, 2024
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  3. REplace custom check_<assembly>_cpus functions

    @jfy133
    jfy133 committed Oct 17, 2024
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Commits on Oct 21, 2024

  1. Update schema, fix empty list in tag names, fix missing parameter def… 

    …ault
    @jfy133
    jfy133 committed Oct 21, 2024
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  2. Fix gtdbtk default value incompatibility

    @jfy133
    jfy133 committed Oct 21, 2024
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  3. Fix check for group column in input

    @jfy133
    jfy133 committed Oct 21, 2024
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  4. Remove misleading error messages and allow more string types in run c… 

    …olumn
    @jfy133
    jfy133 committed Oct 21, 2024
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  5. Use correct input for assembly input and improve schema

    @jfy133
    jfy133 committed Oct 21, 2024
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  6. Use more workable Zenodo link for CheckM database

    @jfy133
    jfy133 committed Oct 21, 2024
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  7. Sync nextflow schema with nextflow.config

    @jfy133
    jfy133 committed Oct 21, 2024
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  8. Update to Zenodo URL also in test config

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

  1. Change pplacer paramter to integer and fix useram default to boolean … 

    …default
    @jfy133
    jfy133 committed Oct 22, 2024
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  2. Fix citations indentitation

    @jfy133
    jfy133 committed Oct 22, 2024
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