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Standardize conversion workflow #369

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Standardize conversion workflow #369

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Commits on Aug 19, 2024

  1. comment out for development

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Aug 19, 2024
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  2. refact modules for STAR aligner

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Aug 19, 2024
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  3. directly pass txp2gene

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Aug 19, 2024
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  4. simplify module lines

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Aug 19, 2024
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  5. emit h5ad on starsolo

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Aug 19, 2024
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  6. add versions emition

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Aug 19, 2024
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  7. update module to use templates and cleanup way of priting versions

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Aug 19, 2024
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Commits on Aug 20, 2024

  1. fix h5ad generator script

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Aug 20, 2024
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  2. simplify check

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Aug 20, 2024
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Commits on Aug 21, 2024

  1. Fix h5ad structure

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Aug 21, 2024
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Commits on Aug 30, 2024

  1. updated concat module

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Aug 30, 2024
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  2. workflow misses emptydrops and seurat & mtx conversion modules

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Aug 30, 2024
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Commits on Sep 12, 2024

  1. start emptydrops cellbender subworkflow

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Sep 12, 2024
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Commits on Sep 13, 2024

  1. fix paths

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Sep 13, 2024
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  2. started the anndatar standardization module

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Sep 13, 2024
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  3. concat h5ad with anndatar h5ad

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Sep 13, 2024
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  4. update tag information

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Sep 13, 2024
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  5. update tags

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Sep 13, 2024
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  6. module is only to convert to rds

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Sep 13, 2024
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  7. update directives

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Sep 13, 2024
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  8. update comments

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Sep 13, 2024
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  9. add cellbender to workflow

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Sep 13, 2024
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  10. start organisation of files

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Sep 13, 2024
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Commits on Sep 26, 2024

  1. fix file naming

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Sep 26, 2024
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  2. resolve emptydrops naming

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Sep 26, 2024
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  3. also convert emptydrops filter matrices

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Sep 26, 2024
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  4. move files to BKP since they will be replaced

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Sep 26, 2024
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  5. add conversion for alevin

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Sep 26, 2024
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  6. re-organise star modules

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Sep 26, 2024
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Commits on Sep 27, 2024

  1. fixed publishDir directives

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Sep 27, 2024
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Commits on Sep 30, 2024

  1. add h5ad conversion module

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Sep 30, 2024
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  2. integrate to mtx_conversion module 

    currently receiving the error: 'H5AD encoding information is missing. This file may have been created with Python anndata<0.8.0.'
    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Sep 30, 2024
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  3. reorganize module levels and fix docker image

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Sep 30, 2024
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  4. reorganize star modules

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Sep 30, 2024
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Commits on Oct 4, 2024

  1. re-structure and include cellranger

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Oct 4, 2024
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  2. add alevin to new structure

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Oct 4, 2024
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  3. add star to new structure

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Oct 4, 2024
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  4. Add kallisto standard workflow to structure

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Oct 4, 2024
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  5. Account for non-standard kallisto workflows

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Oct 4, 2024
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  6. Simplify alevin template

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Oct 4, 2024
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Commits on Oct 7, 2024

  1. reorganise star template

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Oct 7, 2024
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Commits on Oct 30, 2024

  1. write uncompressed 

    Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
    @fmalmeida @grst
    fmalmeida and grst authored Oct 30, 2024
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  2. use .astype(str) 

    Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
    @fmalmeida @grst
    fmalmeida and grst authored Oct 30, 2024
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  3. simplify iteration 

    Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
    @fmalmeida @grst
    fmalmeida and grst authored Oct 30, 2024
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  4. perform join left operation 

    Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
    @fmalmeida @grst
    fmalmeida and grst authored Oct 30, 2024
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  5. do not compress output h5ad 

    Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
    @fmalmeida @grst
    fmalmeida and grst authored Oct 30, 2024
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  6. perform join left operation 

    Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
    @fmalmeida @grst
    fmalmeida and grst authored Oct 30, 2024
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  7. not compress h5ad output

    @fmalmeida
    fmalmeida committed Oct 30, 2024
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  8. simplify iteration

    @fmalmeida
    fmalmeida committed Oct 30, 2024
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  9. simplify index iteration

    @fmalmeida
    fmalmeida committed Oct 30, 2024
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  10. fix unmatched parenthesis

    @fmalmeida
    fmalmeida committed Oct 30, 2024
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  11. fix use of igenomes ... pipeline was not properly selecting igenomes … 

    …options
    @fmalmeida
    fmalmeida committed Oct 30, 2024
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  12. correct values parsing

    @fmalmeida
    fmalmeida committed Oct 30, 2024
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  13. fix container registry

    @fmalmeida
    fmalmeida committed Oct 30, 2024
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  14. do not save versions files

    @fmalmeida
    fmalmeida committed Oct 30, 2024
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  15. also convert concat h5ads

    @fmalmeida
    fmalmeida committed Oct 30, 2024
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  16. manage subdirectory in publishDir

    @fmalmeida
    fmalmeida committed Oct 30, 2024
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  17. match template scripts with new publishDir

    @fmalmeida
    fmalmeida committed Oct 30, 2024
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  18. have outputs separated

    @fmalmeida
    fmalmeida committed Oct 30, 2024
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  19. make parsing inside sub-workflow

    @fmalmeida
    fmalmeida committed Oct 30, 2024
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  20. added kallisto to correct structure

    @fmalmeida
    fmalmeida committed Oct 30, 2024
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  21. correct mix of channels

    @fmalmeida
    fmalmeida committed Oct 30, 2024
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  22. correct for cellranger multi

    @fmalmeida
    fmalmeida committed Oct 30, 2024
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  23. correct stub

    @fmalmeida
    fmalmeida committed Oct 30, 2024
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  24. remove glob in txp2gene

    @fmalmeida
    fmalmeida committed Oct 30, 2024
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  25. added small comment to local modules

    @fmalmeida
    fmalmeida committed Oct 30, 2024
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