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Add support for generating taxprofiler/funcscan input samplesheets for preprocessed FASTQs/FASTAs #688

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Add support for generating taxprofiler/funcscan input samplesheets for preprocessed FASTQs/FASTAs #688

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Commits on Oct 10, 2024

  1. first draft push with TODOs

    @vagkaratzas
    vagkaratzas committed Oct 10, 2024
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  2. first attempt, files not yet being published in outdir

    @vagkaratzas
    vagkaratzas committed Oct 10, 2024
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  3. 4 conditions for different short reads outdirs

    @vagkaratzas
    vagkaratzas committed Oct 10, 2024
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  4. Add funcscan code

    @jasmezz
    jasmezz committed Oct 10, 2024
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  5. Generate multiple samplesheets

    @jasmezz
    jasmezz committed Oct 10, 2024
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  6. Update multi-samplesheet generation

    @jasmezz
    jasmezz committed Oct 10, 2024
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Commits on Oct 14, 2024

  1. Update docs [skip ci] 

    Co-authored-by: James A. Fellows Yates <[email protected]>
    @jasmezz @jfy133
    jasmezz and jfy133 authored Oct 14, 2024
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Commits on Oct 15, 2024

  1. Added channelToSamplesheet function to subworkflow, added nf-test (no… 

    …t run yet)
    @vagkaratzas
    vagkaratzas committed Oct 15, 2024
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  2. Validate samplesheet generation parameters, null defaults,

    @vagkaratzas
    vagkaratzas committed Oct 15, 2024
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  3. nf-test updated (no snapshot yet)

    @vagkaratzas
    vagkaratzas committed Oct 15, 2024
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  4. Update function and minor tweaks

    @jfy133
    jfy133 committed Oct 15, 2024
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  5. Merge branch 'dev' into samplsheet-for-taxprofiler

    @jfy133
    jfy133 authored Oct 15, 2024
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  6. Put the if/else within the function, not as an argument to the function

    @jfy133
    jfy133 committed Oct 15, 2024
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  7. Fix name of file,remove duplicated check

    @jfy133
    jfy133 committed Oct 15, 2024
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  8. Only check save_clipped_reads if taxprofiler in pipeline list

    @jfy133
    jfy133 committed Oct 15, 2024
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Commits on Oct 16, 2024

  1. Fix logic for generating taxprofiler paths; make new channel to pass … 

    …correct assemblies files (Funcsan)
    @jfy133
    jfy133 committed Oct 16, 2024
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Commits on Oct 24, 2024

  1. Merge remote-tracking branch 'upstream/dev' into samplsheet-for-taxpr… 

    …ofiler
    @jfy133
    jfy133 committed Oct 24, 2024
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  2. Compelte template merge

    @jfy133
    jfy133 committed Oct 24, 2024
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Commits on Oct 27, 2024

  1. Merge branch 'dev' into samplsheet-for-taxprofiler

    @jfy133
    jfy133 authored Oct 27, 2024
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