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Update SPAdes module to official nf-core and version bump #666

Merged
merged 26 commits into from
Oct 22, 2024
Merged

Update SPAdes module to official nf-core and version bump #666

merged 26 commits into from
Oct 22, 2024

Commits on Sep 9, 2024

  1. Replace local spades modules with official nf-core version (missing f… 

    …ix CPU trick)
    @jfy133
    jfy133 committed Sep 9, 2024
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  2. Update CHANGELOG.md

    @jfy133
    jfy133 committed Sep 9, 2024
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Commits on Sep 10, 2024

  1. Fix output docs

    @jfy133
    jfy133 committed Sep 10, 2024
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  2. Make sure warnings log also gets a prefix

    @jfy133
    jfy133 committed Sep 10, 2024
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  3. Merge branch 'dev' into bump-metaspades

    @jfy133
    jfy133 authored Sep 10, 2024
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Commits on Sep 12, 2024

  1. Fix a syntax error (Ben made me do it)

    @jfy133
    jfy133 committed Sep 12, 2024
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Commits on Sep 20, 2024

  1. Switch local MEGAHIT to official nf-core one

    @jfy133
    jfy133 committed Sep 20, 2024
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  2. Fix wrongly set branch

    @jfy133
    jfy133 committed Sep 20, 2024
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  3. Merge branch 'dev' into bump-metaspades

    @jfy133
    jfy133 authored Sep 20, 2024
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  4. Fix linting

    @jfy133
    jfy133 authored Sep 20, 2024
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Commits on Oct 3, 2024

  1. Merge branch 'dev' into bump-metaspades

    @jfy133
    jfy133 committed Oct 3, 2024
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  2. Replace assembler single-use fix-cpu functions with single line defin… 

    …itions
    @jfy133
    jfy133 committed Oct 3, 2024
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  3. Ensure checkmax is still used

    @jfy133
    jfy133 committed Oct 3, 2024
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  4. Specify also module changes

    @jfy133
    jfy133 committed Oct 3, 2024
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Commits on Oct 4, 2024

  1. Lets see if SPAdes now works with fusion with the new container...

    @jfy133
    jfy133 committed Oct 4, 2024
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Commits on Oct 22, 2024

  1. Fix GTDBTk Url in schema

    @jfy133
    jfy133 committed Oct 22, 2024
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  2. Merge branch 'dev' into bump-metaspades

    @jfy133
    jfy133 committed Oct 22, 2024
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  3. Update CHANGELOG

    @jfy133
    jfy133 committed Oct 22, 2024
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  4. Merge branch 'dev' into bump-metaspades

    @jfy133
    jfy133 authored Oct 22, 2024
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  5. Make sure meta mode is executed with the new module

    @jfy133
    jfy133 committed Oct 22, 2024
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  6. Fix linting

    @jfy133
    jfy133 committed Oct 22, 2024
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  7. Remove a TODO

    @jfy133
    jfy133 committed Oct 22, 2024
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  8. Add MEGAHIT prefix to ensure MEGAHIT at the beginning of the input fi… 

    …le name.
    @jfy133
    jfy133 committed Oct 22, 2024
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  9. Re-add memory explicit parameter to MEGAHIT module (inbuilt into SPAd… 

    …es module)
    @jfy133
    jfy133 committed Oct 22, 2024
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  10. Re-add MEGAHIT memory

    @jfy133
    jfy133 committed Oct 22, 2024
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  11. Use HTTPS URL for megahit container

    @jfy133
    jfy133 committed Oct 22, 2024
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