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kallisto|bustools 0.28.2 update #294

Merged
merged 39 commits into from
Mar 7, 2024
Merged

kallisto|bustools 0.28.2 update #294

merged 39 commits into from
Mar 7, 2024

Commits on Jan 10, 2024

  1. Merge pull request nf-core#283 from nf-core/dev 

    Release v2.5.0
    @grst
    grst authored Jan 10, 2024
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Commits on Jan 22, 2024

  1. first commit: bump up kb versions

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

  1. Merge pull request nf-core#293 from nf-core/dev 

    Patch release v2.5.1
    @grst
    grst authored 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. renaming parameters

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

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

    @gennadyFauna
    gennadyFauna committed Jan 29, 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. de-duplicating txp2gene args (lint complains)

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

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

    @gennadyFauna
    gennadyFauna committed Feb 13, 2024
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  4. 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. Merge branch 'dev' into kb_update

    @grst
    grst committed Feb 14, 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 Mar 4, 2024

  1. version bump

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

    @nf-core-bot
    nf-core-bot committed Mar 4, 2024
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Commits on Mar 7, 2024

  1. Merge branch 'dev' into kb_update

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

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

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

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

    @grst
    grst committed Mar 7, 2024
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