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Release v2.6.0 #318

Merged
merged 135 commits into from
May 7, 2024
Merged

Release v2.6.0 #318

merged 135 commits into from
May 7, 2024

Commits on Jan 19, 2024

  1. add nf-test for alevin aligner

    @fmalmeida
    fmalmeida committed Jan 19, 2024
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  2. adding nf-test for star aligner

    @fmalmeida
    fmalmeida committed Jan 19, 2024
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Commits on Jan 22, 2024

  1. Merge branch 'dev' of https://github.com/nf-core/scrnaseq into 91-imp… 

    …lement-tests-with-nf-test
    @fmalmeida
    fmalmeida committed Jan 22, 2024
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  2. first commit: bump up kb versions

    @gennadyFauna
    gennadyFauna committed Jan 22, 2024
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Commits on Jan 23, 2024

  1. Bump version to 2.6.0dev

    @grst
    grst committed Jan 23, 2024
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  2. Merge pull request #295 from nf-core/bump-version 

    Bump version to 2.6.0dev
    @grst
    grst authored Jan 23, 2024
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  3. add nf-tests for cellranger aligner

    @fmalmeida
    fmalmeida committed Jan 23, 2024
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  4. add nf-test for kallisto aligner

    @fmalmeida
    fmalmeida committed Jan 23, 2024
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Commits on Jan 24, 2024

  1. Merge branch 'nf-core:master' into kb_update

    @gennadyFauna
    gennadyFauna authored Jan 24, 2024
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Commits on Jan 29, 2024

  1. Template update for nf-core/tools version 2.12

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    nf-core-bot committed Jan 29, 2024
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  2. renaming parameters

    @gennadyFauna
    gennadyFauna committed Jan 29, 2024
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  3. Memory arg might need to be before fastq list?

    @gennadyFauna
    gennadyFauna committed Jan 29, 2024
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  4. Update main.nf

    @gennadyFauna
    gennadyFauna committed Jan 29, 2024
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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. Fixing issue #297

    @heylf
    heylf committed Feb 2, 2024
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  2. fixed workflow conversions to work with star align results

    fmalmeida committed Feb 2, 2024
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  3. fix issue 299

    @heylf
    heylf committed Feb 2, 2024
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  4. Fix for Issue 229

    @heylf
    heylf 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 10, 2024

  1. Removed t2g versions call 

    That is not really what this argument does – it just concatenates the gene_version and transcript_version fields to IDs.
    @gennadyFauna
    gennadyFauna committed Feb 10, 2024
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Commits on Feb 12, 2024

  1. removing t2g.py 

    The txp2gene file should really be generated by kallisto|bustools. The t2g.py script generates a 3-column rather than 7-column t2g, which seems to be incompatible with kb count.
    @gennadyFauna
    gennadyFauna committed Feb 12, 2024
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  2. Remove txp2gene.collect() call 

    This .collect() is incompatible with passing in an existing t2g, and superfluous given the .collect() after the kb ref call.
    @gennadyFauna
    gennadyFauna committed Feb 12, 2024
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  3. add t1c/t2c parameters to schema 

    t1c and t2c are required to run nac and lamanno count workflows. Since they are already defined when running kb ref, they cannot be easily defined through ext.args when using an existing reference
    @gennadyFauna
    gennadyFauna committed Feb 12, 2024
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  4. Fixed kallisto_gene_map documentation 

    scrnaseq does not actually use kallisto_gene_map anywhere.
Changed kallisto icon from a salmon to a rainbow (there is no bear icon, but bustools uses the Pink Floyd-esque prism image, so it seems most appropriate)
    @gennadyFauna
    gennadyFauna committed Feb 12, 2024
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  5. Update nextflow_schema.json

    @gennadyFauna
    gennadyFauna committed Feb 12, 2024
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Commits on Feb 13, 2024

  1. Merge branch 'dev' into nf-core-template-merge-2.12

    @grst
    grst committed Feb 13, 2024
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  2. Update modules

    @grst
    grst committed Feb 13, 2024
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  3. Fix pre-commit

    @grst
    grst committed Feb 13, 2024
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  4. Fix lint

    @grst
    grst committed Feb 13, 2024
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  5. Merge pull request #298 from nf-core/nf-core-template-merge-2.12 

    Important! Template update for nf-core/tools v2.12
    @grst
    grst authored Feb 13, 2024
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  6. update tests

    @fmalmeida
    fmalmeida committed Feb 13, 2024
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  7. update ci.yml for nf-test

    @fmalmeida
    fmalmeida committed Feb 13, 2024
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  8. also allow on push

    @fmalmeida
    fmalmeida committed Feb 13, 2024
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  9. add if and remove needs

    @fmalmeida
    fmalmeida committed Feb 13, 2024
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  10. modify names to have only aligner name

    @fmalmeida
    fmalmeida committed Feb 13, 2024
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  11. fix quotation

    @fmalmeida
    fmalmeida committed Feb 13, 2024
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  12. removing quotations

    @fmalmeida
    fmalmeida committed Feb 13, 2024
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  13. de-duplicating txp2gene args (lint complains)

    @gennadyFauna
    gennadyFauna committed Feb 13, 2024
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  14. Update nextflow_schema.json

    @gennadyFauna
    gennadyFauna committed Feb 13, 2024
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  15. txp2gene has to be moved if it's shared

    @gennadyFauna
    gennadyFauna committed Feb 13, 2024
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  16. adding explicit t1c and t2c arguments for kb 

    Maybe it is possible to somehow inject them with ext.args, but this is a fairly standard pipeline option, and should probably be exposed.
    @gennadyFauna
    gennadyFauna committed Feb 13, 2024
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Commits on Feb 14, 2024

  1. updated tests to use assertAll()

    @fmalmeida
    fmalmeida committed Feb 14, 2024
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  2. update changelog

    @fmalmeida
    fmalmeida committed Feb 14, 2024
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  3. Merge branch 'dev' of https://github.com/nf-core/scrnaseq into 91-imp… 

    …lement-tests-with-nf-test
    @fmalmeida
    fmalmeida committed Feb 14, 2024
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  4. Merge pull request #291 from nf-core/91-implement-tests-with-nf-test 

    Adding nf-tests for pipeline. Currently, only the main aligners: alevin, kallisto, star and cellranger.
    @fmalmeida
    fmalmeida authored Feb 14, 2024
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  5. Merge branch 'dev' into heylf-dev

    @grst
    grst committed Feb 14, 2024
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  6. Merge branch 'dev' into kb_update

    @grst
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  7. 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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  8. update shared nf-test config

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

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

    @fmalmeida
    fmalmeida committed Feb 14, 2024
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  11. 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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  12. fix naming of generated files (kallisto)

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

    @fmalmeida
    fmalmeida committed Feb 14, 2024
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  14. 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 Feb 20, 2024

  1. Template update for nf-core/tools version 2.13

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    nf-core-bot committed Feb 20, 2024
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Commits on Feb 23, 2024

  1. harmonizing with PR while that's in progress

    @gennadyFauna
    gennadyFauna committed Feb 23, 2024
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  2. Update nextflow_schema.json

    @gennadyFauna
    gennadyFauna committed Feb 23, 2024
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  3. Update main.nf

    @gennadyFauna
    gennadyFauna committed Feb 23, 2024
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Commits on Feb 24, 2024

  1. Update kallisto_bustools.nf

    @gennadyFauna
    gennadyFauna committed Feb 24, 2024
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  2. Update kallisto_bustools.nf

    @gennadyFauna
    gennadyFauna committed Feb 24, 2024
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Commits on Feb 27, 2024

  1. docker container update

    @gennadyFauna
    gennadyFauna committed Feb 27, 2024
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  2. manually updated md5s 

    this is not a real snapshot
    @gennadyFauna
    gennadyFauna committed Feb 27, 2024
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  3. Update main_pipeline_kallisto.test.snap

    @gennadyFauna
    gennadyFauna committed Feb 27, 2024
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  4. update mtx construction 

    mtx should take in nascent/ambiguous/mature matrices.
The genes.names txt contains gene names, which are typically what is desired (e.g. cellranger has names rather than IDs)
    @gennadyFauna
    gennadyFauna committed Feb 27, 2024
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  5. update seurat too

    @gennadyFauna
    gennadyFauna committed Feb 27, 2024
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  6. this must have gotten fixed a few kb versions ago

    @gennadyFauna
    gennadyFauna committed Feb 27, 2024
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  7. ...and the R changes have to be updated in md5

    @gennadyFauna
    gennadyFauna committed Feb 27, 2024
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  8. correcting var

    @gennadyFauna
    gennadyFauna committed Feb 27, 2024
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  9. features too

    @gennadyFauna
    gennadyFauna committed Feb 27, 2024
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Commits on Feb 29, 2024

  1. Template update for nf-core/tools version 2.13.1

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    nf-core-bot committed Feb 29, 2024
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Commits on Mar 4, 2024

  1. version bump

    EC2 Default User committed Mar 4, 2024
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  2. [automated] Fix linting with Prettier

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    nf-core-bot committed Mar 4, 2024
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Commits on Mar 5, 2024

  1. Merge branch 'dev' into nf-core-template-merge-2.13.1

    @grst
    grst committed Mar 5, 2024
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Commits on Mar 6, 2024

  1. WIP cleanup after tempalte update

    @grst
    grst committed Mar 6, 2024
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Commits on Mar 7, 2024

  1. Move parameter validation to nextflow schema

    @grst
    grst committed Mar 7, 2024
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  2. Enable workflow

    @grst
    grst committed Mar 7, 2024
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  3. pre-commit

    @grst
    grst committed Mar 7, 2024
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  4. Fix CI

    @grst
    grst committed Mar 7, 2024
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  5. Update modules and fix linting

    @grst
    grst committed Mar 7, 2024
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  6. Fix multiqc

    @grst
    grst committed Mar 7, 2024
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  7. Fix nf-test

    @grst
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  8. Fix nf-test

    @grst
    grst committed Mar 7, 2024
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  9. Fix lint

    @grst
    grst committed Mar 7, 2024
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  10. attempt ignore monochromeLogs lint

    @grst
    grst committed Mar 7, 2024
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  11. attempt ignore monochromeLogs lint

    @grst
    grst committed Mar 7, 2024
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  12. Update comments

    @grst
    grst committed Mar 7, 2024
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  13. Merge pull request #309 from nf-core/nf-core-template-merge-2.13.1 

    Important! Template update for nf-core/tools v2.13.1
    @grst
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  14. Merge branch 'dev' into 81-call-empty-droplets

    @grst
    grst authored Mar 7, 2024
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  15. Merge branch 'dev' into dev

    @grst
    grst authored Mar 7, 2024
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  16. Merge branch 'dev' into kb_update

    @grst
    grst authored Mar 7, 2024
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  17. Delete .nf-test.log

    @grst
    grst authored Mar 7, 2024
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  18. Update nextflow_schema.json

    @grst
    grst authored Mar 7, 2024
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  19. Fix nextflow schema

    @grst
    grst committed Mar 7, 2024
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  20. Update changelog

    @grst
    grst committed Mar 7, 2024
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  21. Merge pull request #294 from gennadyFauna/kb_update 

    kallisto|bustools 0.28.2 update
    @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 <mail@gregor-sturm.de>
    @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. Update modules

    @grst
    grst committed Mar 13, 2024
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  2. Merge remote-tracking branch 'origin/dev' into dev

    @grst
    grst committed Mar 13, 2024
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  3. Update CHANGELOG

    @grst
    grst committed Mar 13, 2024
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  4. Merge pull request #300 from heylf/dev 

    Fix to issue 299 and 297
    @grst
    grst authored Mar 13, 2024
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  5. Merge branch 'dev' into 81-call-empty-droplets

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

    fmalmeida committed Mar 13, 2024
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  7. remove unused parameter

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

    …& nac) workflows
    fmalmeida committed Mar 13, 2024
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  9. 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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  6. Merge pull request #301 from nf-core/81-call-empty-droplets 

    Fix issue 81, "call empty droplets"
    @fmalmeida
    fmalmeida authored Mar 18, 2024
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Commits on Apr 16, 2024

  1. updated modules with 'nf-core modules update'

    @fmalmeida
    fmalmeida committed Apr 16, 2024
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  2. update changelog

    @fmalmeida
    fmalmeida committed Apr 16, 2024
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  3. parse filtered / raw channels

    @fmalmeida
    fmalmeida committed Apr 16, 2024
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  4. update nf-test snaps

    @fmalmeida
    fmalmeida committed Apr 16, 2024
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  5. default to true

    @fmalmeida
    fmalmeida committed Apr 16, 2024
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  6. Merge pull request #317 from nf-core/316-update-cellranger-modules-to… 

    …-latest-nf-coremodules-versions

316 update cellranger modules to latest nf coremodules versions
    @grst
    grst authored Apr 16, 2024
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  7. bump version and update changelog

    @grst
    grst committed Apr 16, 2024
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Commits on Apr 18, 2024

  1. Update download_pipeline.yml

    @grst
    grst authored Apr 18, 2024
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  2. [automated] Fix linting with Prettier

    @nf-core-bot
    nf-core-bot committed Apr 18, 2024
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  3. Merge pull request #320 from nf-core/release-2.6.0 

    Bump version to 2.6.0
    @grst
    grst authored Apr 18, 2024
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Commits on Apr 30, 2024

  1. re-added celranger-arc backwards compatibility

    @fmalmeida
    fmalmeida committed Apr 30, 2024
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  2. Merge pull request #321 from nf-core/add-cellrangerarc-snippet-back 

    Add cellrangerarc snippet back
    @grst
    grst authored Apr 30, 2024
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