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Commits on Feb 6, 2023

• fix viash-test ci

  rcannood

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• fix ci

  rcannood

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Commits on Feb 3, 2023

• proposed cleanup of actions (openpipelines-bio#275)

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  rcannood

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• Explicitly set var and obs columns while filtering with counts. (openpipelines-bio#262)

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  DriesSchaumont

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  9192dbe

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• Fix logging message in 'do_filter' when filtering using .var column (openpipelines-bio#264)

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  DriesSchaumont

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  1e9f1c6

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• Remove bin scripts (openpipelines-bio#258)

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  DriesSchaumont

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  rcannood

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Commits on Feb 1, 2023

• Bump tj-actions/changed-files from 35.4.4 to 35.5.0 (openpipelines-bio#271)

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  dependabot[bot]

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Commits on Jan 23, 2023

• Bump tj-actions/changed-files from 35.4.3 to 35.4.4 (openpipelines-bio#260)

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Commits on Jan 19, 2023

• Bump tj-actions/changed-files from 35.4.1 to 35.4.3 (openpipelines-bio#259)

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  dependabot[bot]

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• calculcate_qc_metrics: fix top_n_vars argument type

  DriesSchaumont

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  b1b2fc3

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Commits on Jan 18, 2023

• Add qc metrics to pipeline (openpipelines-bio#257)

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  DriesSchaumont

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• Add more arguments to RNA multisample pipeline. (openpipelines-bio#243)

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  DriesSchaumont

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Commits on Jan 17, 2023

• Cellranger multi: apply gex_chemistry, gex_secondary_analysis, gex_generate_bam, gex_include_introns and gex_expect_cells (openpipelines-bio#248)

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  DriesSchaumont

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• from_bdrhap_to_h5mu: bump R version to 4.2 (openpipelines-bio#256)

  DriesSchaumont

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  641a214

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• Fix filter 10xh5 build (openpipelines-bio#253)

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  DriesSchaumont

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• Implement calculcate_qc_metrics (openpipelines-bio#231)

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  DriesSchaumont

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• Add protein filtering to full pipeline. (openpipelines-bio#236)

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  DriesSchaumont

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• Add github PR template (openpipelines-bio#250)

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  DriesSchaumont

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  rcannood

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• Filter_with_hvg: improve parameter checking and error reporting (openpipelines-bio#241)

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  DriesSchaumont

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Commits on Jan 12, 2023

• Bump tj-actions/changed-files from 35.4.0 to 35.4.1 (openpipelines-bio#245)

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Commits on Jan 10, 2023

• Allow running cellbender_remove_background component directly from script.

  DriesSchaumont

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• Add test for selecting output layer in log1p. (openpipelines-bio#244)

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  DriesSchaumont

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Commits on Jan 9, 2023

• Fix scarches test (openpipelines-bio#242)

  DriesSchaumont

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  f8c8b54

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• Merge branch 'main' of github.com:openpipelines-bio/openpipeline

  rcannood

  committed
  8dffdf8

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• fix description

  rcannood

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  11c1185

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Commits on Jan 6, 2023

• simplify condition

  rcannood

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  1bfa25d

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• Bump tj-actions/changed-files from 35.3.1 to 35.4.0 (openpipelines-bio#240)

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• Merge branch 'main' of github.com:openpipelines-bio/openpipeline

  rcannood

  committed
  9c338d8

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• fix feature info issue in multi_star

  rcannood

  committed
  0bbf184

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Commits on Jan 5, 2023

• Concat: input_id is only required when --mode is 'move'

  DriesSchaumont

  committed
  b84e7e2

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• Add cpus and memory to cellranger mkfastq tests. (openpipelines-bio#239)

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  DriesSchaumont

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• Bump tj-actions/changed-files from 35.2.1 to 35.3.1 (openpipelines-bio#238)

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  dependabot[bot]

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Commits on Jan 4, 2023

• Concat: include file path when reading in a mudata file fails. (openpipelines-bio#237)

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  DriesSchaumont

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Commits on Jan 2, 2023

• Pass cpu and memory parameters when testing cellranger multi (openpipelines-bio#235)

  DriesSchaumont

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  72914dc

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• Bump tj-actions/changed-files from 35.2.0 to 35.2.1 (openpipelines-bio#234)

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