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1.4.0 #63

Merged
merged 27 commits into from
Jul 26, 2024
Merged

1.4.0 #63

merged 27 commits into from
Jul 26, 2024

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pwwang
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@pwwang pwwang commented Jun 26, 2024

  • docs: update Singularity and Apptainer commands to include --writable-tmpfs flag
  • docs: allow collapsing ns/choice items in the docs for processes
  • docker: update Dockerfile to include npm cache configuration to allow the pipeline to run on read-only file system
  • tests: update SeuratPreparing config to use DoubletFinder for doublet detection
  • ci: use latest actions
  • deps: add r-clustree as a dependency in docker environment files
  • deps: update dependencies in docker environment files (python3.10, R4.3)
  • deps: bump biopipen to 0.29.0
  • deps: pin nodejs version to 20 in docker environment files
    • fix(tcr.TCRClusterStats): fix envs.shared_clusters.heatmap_meta being broken by envs.shared_clusters.sample_order (@li.ying@mayo.edu)
    • choir(scrna.SeuratMap2Ref): present better error message when envs.use or values of envs.MapQuery.refdata not in reference (@li.ying@mayo.edu)
    • fix(scrna.MarkersFinder): run PrepSCTFindMarkers when needed
    • choir(scrna.SeuratClustering): use FindClusters to run for multiple resolutions
    • choir(scrna.SeuratSubClustering): use FindClusters to run for multiple resolutions
    • feat(scrna.SeuratClustering): add clustree plot (@li.ying@mayo.edu)
    • feat(scrna.SeuratSubClustering): add clustree plot
    • tests(scrna.SeuratClusterStats): add assertion for clustree plot generation
  • deps: bump biopipen to 0.29.1
    • fix(delim.SampleInfo): fix numbers not split up when each is specified.
    • enh(delim.SampleInfo): make sizes of pie charts proportional to number of samples when each is specified
    • enh(scrna.MarkersFinder): run PrepSCTFindMarkers when necessary before calling FindMarkers
    • feat(scrna.SeuratPreparing): add option to cache Seurat object at different steps
    • feat(scrna.SeuratPreparing): allow doubletfinder to run with a different number of cores
    • chore(scrna.SeuratClustering): record PrepSCTFindMarkers command in sobj@commands
    • tests(scrna.SeuratClusterStats): use less stringent p-value cutoff for DEG/MarkersFinder
    • tests(scrna.SeuratPreparing): add doubletfinder in tests
  • deps: bump biopipen to 0.29.2
    • chore(scrna.SeuratClusterStats): use ident label length to adjust default height for feature plots
    • fix(scrna.MetaMarkers): fix seurat object not updated when expanding cases and run PrepSCTFindMarkers when necessary before calling meta-markers
    • fix(scrna.MarkersFinder): fix fetching command when composing the PrepSCTFindMarkers command
    • fix(scrna_metabolic_landscape): handle null values in for loop in MetabolicFeatures and MetabolicFeaturesIntraSubset for report generation
  • deps: bump biopipen to 0.30.0
    • BREAKING(scrna): move clustree plots from SeuratClustering/SeuratSubClustering to SeuratClusterStats
    • feat(scrna.CellTypeAnnotation): allow to merge/not to merge (envs.merge) the clusters with the same labels predicted
    • feat(scrna.SeuratPreparing): add scDblFinder to detect doublets
    • feat(scrna.SeuratMap2Ref): add envs.skip_if_normalized option to skip normalization if query is already normalized using the same - method as the reference
    • refactor(tcr.Immunarch): source the files for Immunarch scripts for better debugging
    • refactor(scnra.SeuratClustering): refactor the script for better debugging
    • refactor(scnra.SeuratPreparing): refactor the script for better debugging
    • fix(scrna): fix resolution expansion for SeuratClustering and SeuratSubClustering
    • fix(scrna): Fix generating PrepSCTFindMarkers command when no previous commands present
    • tests(scrna.ScFGSEA): fix unavailable urls to GMT files
    • chore(scrna.SeuratMap2Ref): optimize memory usage
    • chore(scrna.MetaMarkers): remove plugin_opts.poplog_max
    • chore(tcr.CloneResidency): improve logging when handling subjects
  • deps: bump biopipen to 0.31.0
    • deps: bump pipen to 0.15
  • deps: bump biopipen to 0.31.1
    • enh(scrna.SeuratMap2Ref): check if reference has SCTModel if SCTransform'ed (likely prepared by old Seurat)
  • deps: bump biopipen to 0.31.2
    • fix(tcr.CDR3AAPhyschem): use sequence from TRB chain only
    • fix(tcr.TCRClustering): fix for multi-chain TCRs, use TRB only if on_multi is false

@pwwang pwwang changed the title 1.3.10 1.4.0 Jul 16, 2024
@pwwang pwwang merged commit 5f3f597 into master Jul 26, 2024
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