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Add Hello-channels, stub for containers etc and reorder training modules #391

Merged
merged 33 commits into from
Oct 22, 2024
Merged

Add Hello-channels, stub for containers etc and reorder training modules #391

merged 33 commits into from
Oct 22, 2024

Commits on Oct 10, 2024

  1. Reorder training modules

    @vdauwera
    vdauwera committed Oct 10, 2024
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  2. Remove GVCF and joint genotyping from Hello-GATK 

    Simplify Part 2 by making regular VCFs and removing the joint genotyping step.
    @vdauwera
    vdauwera committed Oct 10, 2024
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  3. Start updating the channels stub 

    Stub in the direct command invocations, add in switch to GVCF, remove basic GATK steps
    @vdauwera
    vdauwera committed Oct 10, 2024
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  4. Add introductory explanations 

    Added more intro explanations to Hello GATK + equivalent for Hello Channels
    @vdauwera
    vdauwera committed Oct 10, 2024
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Commits on Oct 17, 2024

  1. Added joint genotyping to Hello-channels 

    Also improved explanations + tweaked order of steps
    @vdauwera
    vdauwera committed Oct 17, 2024
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  2. Prettier fixes

    @vdauwera
    vdauwera committed Oct 17, 2024
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  3. Merge branch 'master' into gvda-hello-channels

    @vdauwera
    vdauwera authored Oct 17, 2024
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  4. Finish converting the splitText to splitCsv 

    change filename extension + add .flatten()
    @vdauwera
    vdauwera committed Oct 17, 2024
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  5. Merge branch 'gvda-hello-channels' of https://github.com/nextflow-io/… 

    …training into gvda-hello-channels
    @vdauwera
    vdauwera committed Oct 17, 2024
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  6. Prettier fixes 

    killing me with the whitespace
    @vdauwera
    vdauwera committed Oct 17, 2024
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Commits on Oct 19, 2024

  1. Merge branch 'master' into gvda-hello-channels

    @vdauwera
    vdauwera committed Oct 19, 2024
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  2. Update TOC in YML file

    @vdauwera
    vdauwera committed Oct 19, 2024
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  3. Fix TOC and update ordinals

    @vdauwera
    vdauwera committed Oct 19, 2024
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  4. Add stubs for planned modules and update order/ordinals

    @vdauwera
    vdauwera committed Oct 19, 2024
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  5. Prettier fixes

    @vdauwera
    vdauwera committed Oct 19, 2024
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Commits on Oct 20, 2024

  1. Merge branch 'master' into gvda-hello-channels

    @vdauwera
    vdauwera committed Oct 20, 2024
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  2. More explanations to GATK docs

    @vdauwera
    vdauwera committed Oct 20, 2024
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  3. A few more GATK explanations

    @vdauwera
    vdauwera committed Oct 20, 2024
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  4. Complete explanations for hello gatk 

    still need to update console outputs
    @vdauwera
    vdauwera committed Oct 20, 2024
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Commits on Oct 21, 2024

  1. Improvements to Orientation + Hello World instructions 

    + A few minor changes in ordering of steps (biggest one is now we look at the code before running it, in response to popular demand...)
    @vdauwera
    vdauwera committed Oct 21, 2024
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  2. Tiny addition to introduction

    @vdauwera
    vdauwera committed Oct 21, 2024
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  3. Minor tweaks to Part 3 (GATK) instructions

    @vdauwera
    vdauwera committed Oct 21, 2024
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  4. Formatting fixes and minor language tweaks

    @vdauwera
    vdauwera committed Oct 21, 2024
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  5. Formatting fixes and updated outputs

    @vdauwera
    vdauwera committed Oct 21, 2024
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  6. Minor fixes

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

  1. Language tweak 

    Co-authored-by: Maxime U Garcia <[email protected]>
    @vdauwera @maxulysse
    vdauwera and maxulysse authored Oct 22, 2024
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  2. Improve formatting - Orientation 

    Co-authored-by: Ken Brewer <[email protected]>
    @vdauwera @kenibrewer
    vdauwera and kenibrewer authored Oct 22, 2024
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  3. Improve formatting - Hello World 

    Co-authored-by: Ken Brewer <[email protected]>
    @vdauwera @kenibrewer
    vdauwera and kenibrewer authored Oct 22, 2024
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  4. Improve formatting - Hello Channels 

    Co-authored-by: Ken Brewer <[email protected]>
    @vdauwera @kenibrewer
    vdauwera and kenibrewer authored Oct 22, 2024
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  5. Improve formatting - GATK suggestions batch1 

    Co-authored-by: Ken Brewer <[email protected]>
    @vdauwera @kenibrewer
    vdauwera and kenibrewer authored Oct 22, 2024
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  6. Improve formatting - GATK suggestions batch2 

    Co-authored-by: Ken Brewer <[email protected]>
    @vdauwera @kenibrewer
    vdauwera and kenibrewer authored Oct 22, 2024
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  7. Small fixes + add JG flowchart

    @vdauwera
    vdauwera committed Oct 22, 2024
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  8. A few more formatting fixes

    @vdauwera
    vdauwera committed Oct 22, 2024
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