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Fix issue 81, "call empty droplets" #301

Merged
merged 34 commits into from
Mar 18, 2024
Merged

Fix issue 81, "call empty droplets" #301

merged 34 commits into from
Mar 18, 2024

Commits on Jan 31, 2024

  1. minimum inclusion for module 

    tested only with kallisto aligner (both with and without automated kallisto filtering with bustools --filter parameter)
    fmalmeida committed Jan 31, 2024
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Commits on Feb 1, 2024

  1. update input_type labels

    fmalmeida committed Feb 1, 2024
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Commits on Feb 2, 2024

  1. fixed workflow conversions to work with star align results

    fmalmeida committed Feb 2, 2024
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Commits on Feb 5, 2024

  1. include modifications for working with cellranger

    fmalmeida committed Feb 5, 2024
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Commits on Feb 7, 2024

  1. fix the path of matrices when running non-standard kallisto workflow … 

    …(tested with lamanno)
    fmalmeida committed Feb 7, 2024
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  2. fix spliced/unspliced empty_drops conversion

    fmalmeida committed Feb 7, 2024
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  3. solve number of list levels when having spliced / unspliced

    fmalmeida committed Feb 7, 2024
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Commits on Feb 14, 2024

  1. Merge branch 'dev' of https://github.com/nf-core/scrnaseq into 81-cal… 

    …l-empty-droplets
    fmalmeida committed Feb 14, 2024
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  2. update shared nf-test config

    fmalmeida committed Feb 14, 2024
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  3. update alevin file names

    fmalmeida committed Feb 14, 2024
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  4. update alevin tests to also include the .rds files

    @fmalmeida
    fmalmeida committed Feb 14, 2024
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  5. update the number of tasks that are executed, and include raw/filtere… 

    …d in the testings (cellranger)
    @fmalmeida
    fmalmeida committed Feb 14, 2024
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  6. fix naming of generated files (kallisto)

    @fmalmeida
    fmalmeida committed Feb 14, 2024
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  7. update the amount of tasks and generated file names raw/filtered (star)

    @fmalmeida
    fmalmeida committed Feb 14, 2024
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  8. update gitignore

    @fmalmeida
    fmalmeida committed Feb 14, 2024
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Commits on Feb 15, 2024

  1. add new params to schema

    @fmalmeida
    fmalmeida committed Feb 15, 2024
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Commits on Mar 7, 2024

  1. Merge branch 'dev' into 81-call-empty-droplets

    @grst
    grst authored Mar 7, 2024
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Commits on Mar 8, 2024

  1. Update bin/emptydrops_cell_calling.R 

    gsub .gz only in end of string

Co-authored-by: Gregor Sturm <[email protected]>
    @fmalmeida @grst
    fmalmeida and grst authored Mar 8, 2024
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Commits on Mar 11, 2024

  1. fixing stub snippet

    fmalmeida committed Mar 11, 2024
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  2. fix transposition snippet in new module

    fmalmeida committed Mar 11, 2024
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  3. Merge branch 'dev' of https://github.com/nf-core/scrnaseq into 81-cal… 

    …l-empty-droplets
    fmalmeida committed Mar 11, 2024
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Commits on Mar 12, 2024

  1. fixed problem on loading fasta&gtf from params.genome

    fmalmeida committed Mar 12, 2024
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  2. fixed transposition

    fmalmeida committed Mar 12, 2024
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  3. fixed file used

    fmalmeida committed Mar 12, 2024
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Commits on Mar 13, 2024

  1. Merge branch 'dev' into 81-call-empty-droplets

    @grst
    grst authored Mar 13, 2024
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  2. updating documentation

    fmalmeida committed Mar 13, 2024
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  3. remove unused parameter

    fmalmeida committed Mar 13, 2024
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  4. adjust modules to handle kallisto outputs form non-standard (lamanno … 

    …& nac) workflows
    fmalmeida committed Mar 13, 2024
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  5. when running kallisto non-standard workflow store emptydrops in subdi… 

    …rs to avoid file collision
    fmalmeida committed Mar 13, 2024
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Commits on Mar 18, 2024

  1. update modules to get them from nf-core/modules

    fmalmeida committed Mar 18, 2024
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  2. prettier fix

    @fmalmeida
    fmalmeida committed Mar 18, 2024
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  3. small update as file names changed

    @fmalmeida
    fmalmeida committed Mar 18, 2024
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  4. add ending line

    @fmalmeida
    fmalmeida committed Mar 18, 2024
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  5. update changelog

    @fmalmeida
    fmalmeida committed Mar 18, 2024
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