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Move long read preprocessing into a subworkflow #674

Merged
merged 37 commits into from
Oct 11, 2024
Merged

Move long read preprocessing into a subworkflow #674

merged 37 commits into from
Oct 11, 2024

Commits on Sep 20, 2024

  1. Added modules porechop/abi and chopper for QC of long reads

    adro committed Sep 20, 2024
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  2. Move long read preprocessing into subworkflow, and swapping porechop … 

    …module to porechop/abi
    adro committed Sep 20, 2024
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  3. Remove module import from main workflow, and add PORECHOP_ABI in conf… 

    …/modules.config
    adro committed Sep 20, 2024
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Commits on Sep 24, 2024

  1. Exchange local filtlong module to nf-core/filtlong

    @muabnezor
    muabnezor committed Sep 24, 2024
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  2. Add filtlong and porechop logs to multiqc

    @muabnezor
    muabnezor committed Sep 24, 2024
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  3. Added --longread_preprocessing_tools parameters, to let user specify … 

    …long read preprocessing tools. Currently only has the option to specify porechop_abi, but I decided this is a nice solution for future tools that the user might want to chose among
    @muabnezor
    muabnezor committed Sep 24, 2024
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Commits on Sep 25, 2024

  1. Merge branch 'dev' into move_lr_qc

    @muabnezor
    muabnezor authored Sep 25, 2024
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  2. Update modules/nf-core/filtlong/main.nf 

    Fix linting problem
    @muabnezor
    muabnezor authored Sep 25, 2024
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Commits on Sep 30, 2024

  1. make subworkflow name more verbose

    @muabnezor
    muabnezor committed Sep 30, 2024
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  2. make --longread_adaptertrimming_tool as enum porechop or porechop_abi

    @muabnezor
    muabnezor committed Sep 30, 2024
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  3. Make prefix for porechop/porechop-abi more verbose

    @muabnezor
    muabnezor committed Sep 30, 2024
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  4. lint

    @muabnezor
    muabnezor committed Sep 30, 2024
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Commits on Oct 1, 2024

  1. Change default search pattern for filtlong.log files for the filtlong… 

    …module in multiqc
    @muabnezor
    muabnezor committed Oct 1, 2024
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Commits on Oct 3, 2024

  1. Update CHANGELOG.md 

    Co-authored-by: James A. Fellows Yates <[email protected]>
    @muabnezor @jfy133
    muabnezor and jfy133 authored Oct 3, 2024
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  2. Update CHANGELOG.md 

    Co-authored-by: James A. Fellows Yates <[email protected]>
    @muabnezor @jfy133
    muabnezor and jfy133 authored Oct 3, 2024
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  3. Update nextflow_schema.json 

    Co-authored-by: James A. Fellows Yates <[email protected]>
    @muabnezor @jfy133
    muabnezor and jfy133 authored Oct 3, 2024
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  4. Update conf/modules.config 

    Co-authored-by: James A. Fellows Yates <[email protected]>
    @muabnezor @jfy133
    muabnezor and jfy133 authored Oct 3, 2024
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  5. Update conf/modules.config 

    Co-authored-by: James A. Fellows Yates <[email protected]>
    @muabnezor @jfy133
    muabnezor and jfy133 authored Oct 3, 2024
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  6. Update conf/modules.config 

    Co-authored-by: James A. Fellows Yates <[email protected]>
    @muabnezor @jfy133
    muabnezor and jfy133 authored Oct 3, 2024
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  7. Update nextflow_schema.json 

    Co-authored-by: James A. Fellows Yates <[email protected]>
    @muabnezor @jfy133
    muabnezor and jfy133 authored Oct 3, 2024
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  8. Update nextflow.config 

    Co-authored-by: James A. Fellows Yates <[email protected]>
    @muabnezor @jfy133
    muabnezor and jfy133 authored Oct 3, 2024
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  9. Update subworkflows/local/longread_preprocessing.nf 

    Co-authored-by: James A. Fellows Yates <[email protected]>
    @muabnezor @jfy133
    muabnezor and jfy133 authored Oct 3, 2024
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  10. Update subworkflows/local/longread_preprocessing.nf 

    Co-authored-by: James A. Fellows Yates <[email protected]>
    @muabnezor @jfy133
    muabnezor and jfy133 authored Oct 3, 2024
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  11. Update subworkflows/local/longread_preprocessing.nf 

    Co-authored-by: James A. Fellows Yates <[email protected]>
    @muabnezor @jfy133
    muabnezor and jfy133 authored Oct 3, 2024
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  12. Merge branch 'dev' into move_lr_qc

    @muabnezor
    muabnezor authored Oct 3, 2024
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  13. Linting fix

    @muabnezor
    muabnezor committed Oct 3, 2024
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  14. make porechop-abi default long read adapter trimming tool

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

  1. Fix changelog

    @muabnezor
    muabnezor committed Oct 4, 2024
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  2. Fix porechop_abi pattern in modules.config

    @muabnezor
    muabnezor committed Oct 4, 2024
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  3. Merge branch 'dev' into move_lr_qc

    @muabnezor
    muabnezor authored Oct 4, 2024
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  4. remove chopper citation for now

    @muabnezor
    muabnezor committed Oct 4, 2024
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  5. retrigger checks

    @muabnezor
    muabnezor committed Oct 4, 2024
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  6. Merge branch 'dev' into move_lr_qc

    @muabnezor
    muabnezor authored Oct 4, 2024
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Commits on Oct 11, 2024

  1. Apply suggestions from code review

    @jfy133
    jfy133 authored Oct 11, 2024
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  2. Apply suggestions from code review

    @jfy133
    jfy133 authored Oct 11, 2024
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  3. Add previouysly undocumented output files to docs

    @jfy133
    jfy133 authored Oct 11, 2024
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  4. [automated] Fix code linting

    @nf-core-bot
    nf-core-bot committed Oct 11, 2024
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