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Split ArchR analysis into 2 steps#55

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pennycuda wants to merge 35 commits intodevelophubmapconsortium/sc-atac-seq-pipeline:developfrom pennycuda/archr-stepshubmapconsortium/sc-atac-seq-pipeline:pennycuda/archr-stepsCopy head branch name to clipboard

+913-631

Commits

Commits on May 25, 2023

• Separate out parts of ArchR and update cwl to use first part

  

  Sarah

  committed
  da62daf

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• Add new ArchR separate files

  

  Sarah

  committed
  678f6bc

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Commits on Mar 8, 2024

• split archR analysis

  

  Sarah

  committed
  601bfdd

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• update dockerfile for split analysis

  

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• update docker_images for split analysis

  

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  b5d3ef9

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• update requirements for split analysis

  

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  9eb03b7

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• update cwl for split analysis

  

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  750e74f

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• remove assay flag from json

  

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  d64b02d

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• update cwl for split analysis

  

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  1c8d879

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• add files for split analysis

  

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  9191369

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• formatting fixes

  

  Sarah Schultz

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  6a3a2d6

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• formatting fix

  

  Sarah Schultz

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  16b9d72

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• formatting fix

  

  Sarah Schultz

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  70e8218

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Commits on Mar 9, 2024

• skip unneeded cwl step

  

  Sarah Schultz

  committed
  a50df5e

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• formatting fix

  

  Sarah Schultz

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  510b657

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• typo fix

  

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  d7993d2

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• formatting fix

  

  Sarah Schultz

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  31c55c2

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• output name agreement

  

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  d09aa64

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• typo fix

  

  Sarah Schultz

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  3604c56

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Commits on Mar 10, 2024

• add multiome to utils

  

  Sarah Schultz

  committed
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• formatting fixes and variable name agreement

  

  Sarah Schultz

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  f85b797

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Commits on Mar 11, 2024

• Fix adjust_barcodes for 10X multiome (update to match develop branch)

  

  Sarah Schultz

  committed
  a34b323

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• handle 10x barcode (merge changes from develop branch)

  

  Sarah Schultz

  committed
  229f2e4

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Commits on Apr 3, 2024

• Add step 1 image to step 2

  pennycuda

  committed
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• Only need R image in second ArchR step

  pennycuda

  committed
  1caa2ee

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• Save and load ArchR project

  pennycuda

  committed
  8d6e27a

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• Need ArchRProj directory

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• Add r utils package

  pennycuda

  committed
  ac36a29

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• Update bioconductor and load in R file

  pennycuda

  committed
  b837d95

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• move pdf around

  pennycuda

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  0ad64f8

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• Add plots and update cwl

  pennycuda

  committed
  7ed4893

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• Merge branch 'develop' into pennycuda/archr-steps

  pennycuda

  authored
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• Add legacy comment

  pennycuda

  committed
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• Delete unused files

  pennycuda

  committed
  4694d7f

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Commits on Apr 4, 2024

• why is it telling me these files dont exist

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  committed
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