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cellranger-multi implementation follow-up #332

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fmalmeida opened this issue May 23, 2024 · 0 comments
Open
5 tasks

cellranger-multi implementation follow-up #332

fmalmeida opened this issue May 23, 2024 · 0 comments
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enhancement New feature or request

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@fmalmeida
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fmalmeida commented May 23, 2024

Description of feature

During the inclusion of cellranger-multi on #276 a few TODOs were left to be closed on follow-up PRs.
These are:

  • Include automated checkers for cellranger multi parameter combinations.
    • For example, when VDJ data is given, require VDJ ref. If FFPE, require frna probe sets, etc.
  • validate multi-samplesheet using the same logic as the main samplesheet (using nf-validation)
  • Assess possibility of adding automated "if-else" for the VDJ and GEX index reference building.
  • Assess the inclusion and support of BEAM data
    • Assess execution of emptydrops to CRISPR/BEAM/ANTIBODY modes. Maybe is not relevant and can be filtered?
  • Update cellrangermulti test profiles so that required ensembl reference files are available in nf-core test datasets.

FYI: @grst

@fmalmeida fmalmeida added the enhancement New feature or request label May 23, 2024
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