Standardize conversion workflow#369

Merged

grst merged 114 commits intodevfrom

standardize-conversion-workflow

Dec 2, 2024

Commits on Aug 19, 2024

comment out for development
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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refact modules for STAR aligner
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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directly pass txp2gene
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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simplify module lines
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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emit h5ad on starsolo
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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add versions emition
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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update module to use templates and cleanup way of priting versions
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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Commits on Aug 20, 2024

fix h5ad generator script
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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simplify check
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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Commits on Aug 21, 2024

Fix h5ad structure
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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Commits on Aug 30, 2024

updated concat module
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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workflow misses emptydrops and seurat & mtx conversion modules
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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Commits on Sep 12, 2024

start emptydrops cellbender subworkflow
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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Commits on Sep 13, 2024

fix paths
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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started the anndatar standardization module
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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concat h5ad with anndatar h5ad
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update tag information
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update tags
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module is only to convert to rds
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update directives
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update comments
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add cellbender to workflow
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start organisation of files
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Commits on Sep 26, 2024

fix file naming
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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resolve emptydrops naming
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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also convert emptydrops filter matrices
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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move files to BKP since they will be replaced
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add conversion for alevin
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re-organise star modules
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Commits on Sep 27, 2024

fixed publishDir directives
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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Commits on Sep 30, 2024

add h5ad conversion module
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integrate to mtx_conversion module
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reorganize module levels and fix docker image
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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reorganize star modules
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Commits on Oct 4, 2024

re-structure and include cellranger
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add alevin to new structure
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add star to new structure
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Add kallisto standard workflow to structure
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Account for non-standard kallisto workflows
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Simplify alevin template
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Commits on Oct 7, 2024

reorganise star template
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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Commits on Oct 30, 2024

Commits on Nov 15, 2024

split mtx to h5ad conversion and general conversion, so h5ad is generated separately for all aligners, and then passed for format conversion, custom filter and concat.
fmalmeida
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Commits on Nov 25, 2024

fix star index channel generation
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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fixed tuple size
fmalmeida
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Update kallisto script
grst
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update alevin nf-test and snaps
fmalmeida
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Merge branch 'standardize-conversion-workflow' of https://github.com/nf-core/scrnaseq into standardize-conversion-workflow
fmalmeida
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added singlecellobject export
fmalmeida
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include singlecellexperiment object in nf-test and update namings
fmalmeida
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avoind assessing params from modules
fmalmeida
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add snippet to make values unique
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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Merge branch 'standardize-conversion-workflow' of https://github.com/nf-core/scrnaseq into standardize-conversion-workflow
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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fix star channel parsing
fmalmeida
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Merge branch 'standardize-conversion-workflow' of https://github.com/nf-core/scrnaseq into standardize-conversion-workflow
fmalmeida
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simplified kallisto so non-standardo workflow have spliced and unspliced as layers in the same object
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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Merge branch 'standardize-conversion-workflow' of https://github.com/nf-core/scrnaseq into standardize-conversion-workflow
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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update star nf-test, snaps and file namings
fmalmeida
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Merge branch 'standardize-conversion-workflow' of https://github.com/nf-core/scrnaseq into standardize-conversion-workflow
fmalmeida
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Commits on Nov 26, 2024

fix channel size
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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Fix kallisto mtx script
grst
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add a little comment line
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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updated cellranger nf-test sizes, namings and snaps
fmalmeida
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Update kallisto script (again)
grst
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update kallisto nf-test size, namings and snaps
fmalmeida
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adding versions.yml output for modules CONCAT_H5AD, MTX_TO_H5AD and ANNDATAR_CONVERT
fmalmeida
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correct ifelse order for file renames
fmalmeida
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Commits on Nov 28, 2024

Merge branch 'dev' of https://github.com/nf-core/scrnaseq into standardize-conversion-workflow
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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re-add missing star_align ext.args
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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correct the parsing of getGenomeAttribute as a nextflow variable, since it is not possible to overwrite params. in the workflow scope
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current version of star is incompatible with the star index available in igenomes
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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add checkIfExists: true to file loading calls
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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remove old conversion scripts
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Commits on Nov 29, 2024

update changelog
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add TODO
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update emptydrops documentation
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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update cellranger snaps
fmalmeida
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Merge branch 'standardize-conversion-workflow' of https://github.com/nf-core/scrnaseq into standardize-conversion-workflow
fmalmeida
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update kallisto snaps
fmalmeida
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update alevin snaps
fmalmeida
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Update modules/local/templates/barcodes.py

fmalmeida
and
grst
authored
fix anndatar to nf-core container
fmalmeida
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add resources control to cellrangermulti testing profile
fmalmeida
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add metadata
fmalmeida
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allow regex to also find cellrangermulti results
fmalmeida
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update cellranger multi nf-test snaps
fmalmeida
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update star nf-test snaps
fmalmeida
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prettier fix
fmalmeida
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avoid fetching star index from iGenomes due version incompatibility
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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Commits on Dec 2, 2024

add .var_names_make_unique() to star code which was missing
zxBIB Almeida,Felipe (GCBDS) EXTERNAL
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