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Adding cellrangermulti subworkflow #276
Commits on Nov 7, 2023
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Commits on Nov 8, 2023
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Commits on Nov 15, 2023
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Commits on Nov 16, 2023
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include option for unzipping reference files
zxBIB Almeida,Felipe (GCBDS) EXTERNAL committedNov 16, 2023 Configuration menu - View commit details
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Commits on Nov 17, 2023
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zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed
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fmalmeida committed
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Commits on Nov 22, 2023
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input dataset parsing refactored and fixed
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include cellrangermulti outputs in mqc channel
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Commits on Nov 23, 2023
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include option for cellrangermulti in mtx conversion modules
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add files filter for cellranger multi outputs
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include cellranger multi outputs to mtx conversion subworkflow
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Commits on Feb 23, 2024
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update version of cellranger multi module
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include newly required parameters
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Commits on Feb 26, 2024
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Merge branch 'dev' of https://github.com/nf-core/scrnaseq into 247-su…
…pport-for-10x-ffpe-scrna
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include new columns in samplesheet checker
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Commits on Feb 27, 2024
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Commits on Mar 7, 2024
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Commits on Mar 11, 2024
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Merge branch '247-support-for-10x-ffpe-scrna' of https://github.com/n…
…f-core/scrnaseq into 247-support-for-10x-ffpe-scrna
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Commits on Mar 19, 2024
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Merge branch 'dev' of https://github.com/nf-core/scrnaseq into 247-su…
…pport-for-10x-ffpe-scrna
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small dataset cannot run emptydrops
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do not run emptydrops for cellranger arc, and update ch_matrices filt…
…er so empty drops only load raw matrices from cellrager, kallisto and star (alevin has only raw).
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Commits on Mar 20, 2024
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add cellrangermulti in aligners options for conversion and add * to m…
…atch more generically.
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parse cellrangermulti matrix outputs to filter between raw / filtered…
… results,
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fixing filtering option and using correct cellranger-multi mtxs
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Commits on Mar 21, 2024
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revert cellranger modules to latest, without the multi-out-channels a…
…nd add parser in the local subworkflow to perform the file selection
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Commits on Mar 25, 2024
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update modules to latest version
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add a parser for raw/filtered results
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start removing channels related to "deprecated" additional csvs
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add a parser for frna/cmo data from customised, unified, barcodes sam…
…plesheet
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fix if-else and .join() operations
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avoid always writing to allow caching
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Commits on Apr 11, 2024
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converted parsing and split to a module
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fixed cellranger-multi input channel logic
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Commits on Apr 12, 2024
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solved cellranger multi parsing and pipeline execution
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Commits on Apr 15, 2024
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add first cellranger-multi try-out bugfixes
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Commits on Apr 17, 2024
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added frna probeset subset reference and include parsing in module
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frna runs also generate raw data per sample
let's standardize raw = unmultiplexed
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Commits on Apr 18, 2024
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use shared nf-core test-datasets
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update cellranger multi module
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Merge branch 'dev' of https://github.com/nf-core/scrnaseq into 247-su…
…pport-for-10x-ffpe-scrna
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Commits on Apr 22, 2024
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fix file saving and remove outdated workaround on mqc
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add an universal key in cellranger-multi data options map so that par…
…sing in module works fine to differentiate empty / real data
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commit latest editions required in nf-core/module ( must be added in …
…central module )
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make sure the workflow can work with new version of module that does …
…not use 'EMPTY' file for references and rather uses []
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Merge pull request #322 from nf-core/fix-without-gtf
Make it work without specifying GTF file
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include cellrangermulti raw matrices for custom emptydrops filtering
zxBIB Almeida,Felipe (GCBDS) EXTERNAL committedMay 10, 2024 Configuration menu - View commit details
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zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed
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Revert "remove gex_barcode_sample_assignment parameter"
This reverts commit 03a38cd.
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