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Kallisto quantification #1106

Merged
merged 66 commits into from
Nov 15, 2023
Merged

Kallisto quantification #1106

merged 66 commits into from
Nov 15, 2023

Commits on Oct 31, 2023

  1. naive kallisto addition to prepare_genome, following salmon pattern (… 

    …fix later)
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    pinin4fjords committed Oct 31, 2023
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  2. Add kallisto modules

    @pinin4fjords
    pinin4fjords committed Oct 31, 2023
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  3. update schema

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    pinin4fjords committed Oct 31, 2023
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  4. Pass kallisto index in workflow

    @pinin4fjords
    pinin4fjords committed Oct 31, 2023
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  5. Add kallisto quant subworkflow

    @pinin4fjords
    pinin4fjords committed Oct 31, 2023
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  6. [skip ci] next batch of kallisto adaptations

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    pinin4fjords committed Oct 31, 2023
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Commits on Nov 1, 2023

  1. tximport is more generic than just salmon

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    pinin4fjords committed Nov 1, 2023
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  2. Fix kallisto indexing

    @pinin4fjords
    pinin4fjords committed Nov 1, 2023
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  3. [skip ci] Next phase of Kallisto integration

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    pinin4fjords committed Nov 1, 2023
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Commits on Nov 2, 2023

  1. [skip ci] Bump kallisto modules

    @pinin4fjords
    pinin4fjords committed Nov 2, 2023
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  2. [skip ci] rewire for updated kallisto modules

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    pinin4fjords committed Nov 2, 2023
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  3. [skip ci] Make tx2gene.py generic

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    pinin4fjords committed Nov 2, 2023
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  4. [skip ci] Try chatgpt's tidied version of tx2gene.py

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    pinin4fjords committed Nov 2, 2023
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  5. [skip ci] Tidied up and genericised tximport script

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    pinin4fjords committed Nov 2, 2023
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  6. [skip ci] misc compatibility updates

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    pinin4fjords committed Nov 2, 2023
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  7. [skip ci] fix bin/tx2gene.py

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    pinin4fjords committed Nov 2, 2023
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  8. [skip ci] prioritise transcript_id

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    pinin4fjords committed Nov 2, 2023
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  9. [skip ci] final kallisto results handling fixes

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    pinin4fjords committed Nov 2, 2023
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Commits on Nov 3, 2023

  1. more genericisation between kallisto and salmon

    @pinin4fjords
    pinin4fjords committed Nov 3, 2023
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  2. Remove debugging line

    @pinin4fjords
    pinin4fjords committed Nov 3, 2023
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  3. Fix multiqc to avoid imp module error

    @pinin4fjords
    pinin4fjords committed Nov 3, 2023
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  4. Fix process selector

    @pinin4fjords
    pinin4fjords committed Nov 3, 2023
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  5. add kallisto_index default

    @pinin4fjords
    pinin4fjords committed Nov 3, 2023
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  6. Combine kallisto and salmon components

    @pinin4fjords
    pinin4fjords committed Nov 3, 2023
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  7. appease eclint

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    pinin4fjords committed Nov 3, 2023
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  8. [automated] Fix linting with Prettier

    @nf-core-bot
    nf-core-bot committed Nov 3, 2023
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  9. Update CHANGELOG

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    pinin4fjords committed Nov 3, 2023
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  10. Merge branch 'kallisto_quant' of https://github.com/nf-core/rnaseq in… 

    …to kallisto_quant
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    pinin4fjords committed Nov 3, 2023
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  11. blackify

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    pinin4fjords committed Nov 3, 2023
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  12. Don't hardcode tx2gene_file

    @pinin4fjords
    pinin4fjords committed Nov 3, 2023
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  13. syntax fix

    @pinin4fjords
    pinin4fjords authored Nov 3, 2023
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  14. Add some kallisto tests

    @pinin4fjords
    pinin4fjords committed Nov 3, 2023
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  15. Update metro maps

    @pinin4fjords
    pinin4fjords committed Nov 3, 2023
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  16. [skip ci] Fix metro maps

    @pinin4fjords
    pinin4fjords committed Nov 3, 2023
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  17. Update strandedness params for kallisto and salmon

    @pinin4fjords
    pinin4fjords committed Nov 3, 2023
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  18. [skip ci] appease linter

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    pinin4fjords committed Nov 3, 2023
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  19. Fix kallisto publishing

    @pinin4fjords
    pinin4fjords committed Nov 3, 2023
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  20. [skip ci] fix usage.md for Kallisto

    @pinin4fjords
    pinin4fjords committed Nov 3, 2023
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  21. Merge branch 'kallisto_quant' of github.com:nf-core/rnaseq into kalli… 

    …sto_quant
    @pinin4fjords
    pinin4fjords committed Nov 3, 2023
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  22. [automated] Fix linting with Prettier

    @nf-core-bot
    nf-core-bot committed Nov 3, 2023
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  23. Update fraglen defaults

    @pinin4fjords
    pinin4fjords committed Nov 3, 2023
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Commits on Nov 6, 2023

  1. MultiQC needs STDOUT from Kallisto

    @pinin4fjords
    pinin4fjords committed Nov 6, 2023
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  2. Fix Kallisto MultiQC

    @pinin4fjords
    pinin4fjords committed Nov 6, 2023
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  3. Update docs

    @pinin4fjords
    pinin4fjords committed Nov 6, 2023
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  4. [automated] Fix linting with Prettier

    @nf-core-bot
    nf-core-bot committed Nov 6, 2023
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  5. Correct kallisto out path

    @pinin4fjords
    pinin4fjords committed Nov 6, 2023
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  6. Merge branch 'kallisto_quant' of github.com:nf-core/rnaseq into kalli… 

    …sto_quant
    @pinin4fjords
    pinin4fjords committed Nov 6, 2023
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Commits on Nov 7, 2023

  1. Add prefix usage to local modules to facilitate batched runs

    @pinin4fjords
    pinin4fjords committed Nov 7, 2023
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  2. [skip ci] Address easy review feedback

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    pinin4fjords committed Nov 7, 2023
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Commits on Nov 9, 2023

  1. [skip ci] Update config per latest 

    Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
    @pinin4fjords @maxulysse
    pinin4fjords and maxulysse authored Nov 9, 2023
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  2. [skip ci] fix font sizes in metro map file icons

    @pinin4fjords
    pinin4fjords committed Nov 9, 2023
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  3. thank myself to poke ci

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    pinin4fjords committed Nov 9, 2023
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  4. Reflect updated kallisto module

    @pinin4fjords
    pinin4fjords committed Nov 9, 2023
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Commits on Nov 10, 2023

  1. [skip ci] test file not supposed to be there

    @pinin4fjords
    pinin4fjords committed Nov 10, 2023
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  2. Merge branch 'dev' into kallisto_quant

    @pinin4fjords
    pinin4fjords authored Nov 10, 2023
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Commits on Nov 13, 2023

  1. [skip ci] Add Kallisto outputs to Tower yml

    @pinin4fjords
    pinin4fjords committed Nov 13, 2023
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Commits on Nov 14, 2023

  1. Post-review changes

    @drpatelh
    drpatelh committed Nov 14, 2023
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  2. Fix Kallisto sample name rendering in MultiQC

    @drpatelh
    drpatelh committed Nov 14, 2023
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  3. [skip ci] Alphabetically order enum fields for salmon strandedness

    @drpatelh
    drpatelh committed Nov 14, 2023
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  4. [skip ci] Bump module from branch

    @pinin4fjords
    pinin4fjords committed Nov 14, 2023
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  5. Merge branch 'kallisto_quant' of github.com:nf-core/rnaseq into kalli… 

    …sto_quant
    @pinin4fjords
    pinin4fjords committed Nov 14, 2023
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  6. [automated] Fix linting with Prettier

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    nf-core-bot committed Nov 14, 2023
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  7. [skip ci] removed kallisto strandedness as a standalone parameter

    @pinin4fjords
    pinin4fjords committed Nov 14, 2023
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  8. [skip ci] Fix kallisto log file ext

    @pinin4fjords
    pinin4fjords authored Nov 14, 2023
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  9. Fix tiny issue

    @pinin4fjords
    pinin4fjords committed Nov 14, 2023
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  10. [automated] Fix linting with Prettier

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    nf-core-bot committed Nov 14, 2023
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