biopipen

• 💥 [scrna.SeuratMetadataMutater] Move mutaters from in to envs
• 🔥 [scrna.CellsDistribution] Remove unnecessary in.casefile
• 🚑 [scrna.CellTypeAnnotation] Hotfix when envs.hitype_db as a file starts with "hitypedb_"

What's Changed

• 🔖 0.16.5 by @pwwang in https://github.com/pwwang/biopipen/pull/69

Full Changelog: https://github.com/pwwang/biopipen/compare/0.16.4...0.16.5

• 🚑 [scrna.CellTypeAnnotation] Hotfix passing envs.newcol
• ⬆️ Bump pipen-report to 0.12.7

What's Changed

• 0.16.4 by @pwwang in https://github.com/pwwang/biopipen/pull/68

Full Changelog: https://github.com/pwwang/biopipen/compare/0.16.3...0.16.4

• 📝 [scrna_metabolic_landscape] Update docstring
• ✨ [tcr.CDR3AAPhyschem] Allow envs.subset_cols to be separated by comma
• ✨ [scrna.CellTypeAnnotation] Add envs.newcol to keep original idents

What's Changed

• 0.16.3 by @pwwang in https://github.com/pwwang/biopipen/pull/67

Full Changelog: https://github.com/pwwang/biopipen/compare/0.16.2...0.16.3

• 🚨 Add .lintr for R lintr
• ⬆️ Bump pipen-board to 0.11.1
• 💄 [report] Separate enrichr_report
• 💄 [scrna.CellsDistribution] Fix reports
• 💄 [scrna.CellsDistribution] Reorganize report
• 💄 [scrna.MarkersFinder] Reorganize report
• 💄 [scrna.ScFGSEA] Reorganize report
• 💄 [scrna.TopExpressingGenes] Reorganize report
• 🚨 [scrna.TopExpressingGenes] Fix linting issues in script
• 🔧 [scrna.MarkersFinder] Set envs.prefix_each to True by default
• 🔧 [scrna.TopExpressingGenes] Set envs.prefix_each to True by default
• ✨ [scrna.MetaMarkers] Add proc

What's Changed

• 0.16.2 by @pwwang in https://github.com/pwwang/biopipen/pull/66

Full Changelog: https://github.com/pwwang/biopipen/compare/0.16.1...0.16.2

• 🚨 Fix some linting issues
• ⬆️ Bump pipen-board to 0.11
• 🎨 [scrna.CellTypeAnnotation] Rename seurat_clusters.old to seurat_clusters_old to save the old clusters for sctype
• 🐛 [scrna.CellTypeAnnotation] Fix saving annotated cell type to text file for sccatch
• 🎨 [scrna.CellTypeAnnotation] Save old clustering to seurat_clusters_old for sccatch
• 🎨 [scrna.CellTypeAnnotation] Save old clustering to seurat_clusters_old for direct method
• 📝 [scrna.CellTypeAnnotation] Fix links in docs for sccatch
• ✨ [scrna.SeuratClusterStats] Allow envs.exprs.genes to be genes directly (separated by ",")
• 💄 [docs] Update API doc styles for dark mode
• ✨ [tcr.TCRClustering] Save the souce code of GIANA with this package
• ✨ [tcr.TCRClusteringStats] Allow multiple cases
• 📝 [tcr.ImmunarchLoading] Update docstring
• ✨ [utils] Add mutate_helpers to identify expanded, collapsed, emerged and vanished clones
• 🐛 [utils/misc.R] Fix list_setdefault and list_update when value is NULL
• 🐛 [scrna.TopExpressionGenes] Fix expanding cases
• ✨ [scrna.SeuratClustering] Allow envs.FindIntegrationAnchors.reference to be a string separated by comma
• ✨ [scrna.ScFGSEA] Allow multiple cases
• ✨ [scrna.MarkersFinder] Allow to use mutate_helpers in envs.mutaters
• 🎨 [scrna.CellsDistribution] Redesign envs to support multiple cases
• 💄 [tcr.Immunarch] Fix report generation for rarefraction analysis
• 🔧 [tcr.Immunarch] Change envs to be less error prone
• 💄 [scrna.CellsDistribution] Fix reports
• 💄 [scrna.ScFGSEA] Fix reports
• ✅ [tests] Fix tests

What's Changed

• 🔖 0.16.1 by @pwwang in https://github.com/pwwang/biopipen/pull/65

Full Changelog: https://github.com/pwwang/biopipen/compare/0.16.0...0.16.1

• ⬆️ Bump pipen-board to 0.10
• 💄 [docs] Update docs styles
• 🚨 [core/testing] Remove unused importings
• 🎨 [scrna] Rename RNADir to RNAData for input data
• 🐛 [gsea.GSEA] Replace doc.string with doc_string to avoid over parsing by pipen-args
• 🎨 [tcr.Immunarch] Refactor and split into modules
• 🎨 [scrna.CellTypeAnnotation] Rename CellTypeAnnotate to CellTypeAnnotation and add hitype
• 🎨 [tcr.ImmunarchLoading] Make it compatible with immunarch 0.9
• 🎨 [scrna.MakersFinder] Support multiple cases
• 🎨 [scrna.TopExpressionGenes] Support multiple cases
• 🐛 [scrna.RadarPlots] Fix section and devpars not passed to script
• 🐛 [scrna.SeuratClustering] Fix PCA on each sample
• 🎨 [scrna.ExprImpution] Rename from ExprImpute to ExprImputation
• 👷 [scrna.CellTypeAnnotation] Add r-hitype to env_r.yml for testing
• 🐛 [scrna.CellTypeAnnotation] Fix typos for hitype script
• 🐛 [scrna.CellTypeAnnotation] Fix startsWith in hitype script
• 🎨 [scrna_basic] Rename ScrnaBasicAnnotate to ScrnaBasicAnnotation
• 📝 [scrna_basic] Update docs
• 🐛 [cnvkit_pipeline] Fix docker image building
• 📝 [cnvkit_pipeline] Fix docs

• ⬆️ Bump pipen-board to 0.9.1
• ✨ [scrna.RadarPlots] Add process
• 🎨 [tcr.Immunarch] Separate diversity in script into a different file
• ✨ [scrna.TopExpressingGenes] Add process
• 🎨 [scrna.CellsDistribution] Use a different color palette
• 🎨 [scrna.SeuratClusterStats] Warn about heatmap without downsampling

What's Changed

• 0.15.2 by @pwwang in https://github.com/pwwang/biopipen/pull/63

Full Changelog: https://github.com/pwwang/biopipen/compare/0.15.1...0.15.2

• ⬆️ Bump pipen-board to 0.8.0
• ⬆️ Bump pipen-report to 0.12.5 (to fix the pydantic error)
• 🎨 [tcr.CloneResidency] Add indicators during running
• 🎨 [tcr.CloneResidency] Allow multiple cases add mutaters for metadata
• 🐛 [misc.File2Proc] Check if input file exists
• 🎨 [tcr.Immunarch] Allow cases for trackings and add mutaters for metadata

What's Changed

• 🔖 0.15.1 by @pwwang in https://github.com/pwwang/biopipen/pull/62

Full Changelog: https://github.com/pwwang/biopipen/compare/0.15.0...0.15.1

• ⬆️ Bump pipen to 0.10.6
• ⬆️ Bump pipen-board to 0.7.8
• ➖ Retire cmdy at all places (#54)
• ✅ [core.filters] Add run.env to test
• ✅ [core.filters] Add test for dashify=True
• 🎨 [scrna.MarkersFinder] Make envs.sigmarkers case wise for scrna.MarkersFinder (#53)

What's Changed

• 🔖 0.15.0 by @pwwang in https://github.com/pwwang/biopipen/pull/61

Full Changelog: https://github.com/pwwang/biopipen/compare/0.14.3...0.15.0

• ⬆️ Bump pipen to 0.10.5
• 🔧 [scrna_metabolic_landscape] Make proc group options for process readonly
• 🎨 [scrna_metabolic_landscape.MetabolicFeatures] Add indicators during computation

What's Changed

• 🔖 0.14.3 by @pwwang in https://github.com/pwwang/biopipen/pull/60

Full Changelog: https://github.com/pwwang/biopipen/compare/0.14.2...0.14.3

• ⬆️ Bump pipen-board to 0.7.4
• ⬆️ Bump pipen-report to 0.12.3
• ⚡️ Replace do.call with do_call in R scripts to improve performance
• 🐛 [scrna.CellTypeAnnotate] Fix when no cell types is given for direct annotation
• 🐛 [cnv.AneuploidyScore] Fix when envs.cn_tranform is a list of thresholds

What's Changed

• 🔖 0.14.2 by @pwwang in https://github.com/pwwang/biopipen/pull/59

Full Changelog: https://github.com/pwwang/biopipen/compare/0.14.1...0.14.2

• ⬆️ Bump pipen-board to 0.7.3
• ⬆️ Bump other dependencies
• 🎨 [scrna] Add type=int for envs.ncores in docstrings
• 🚑 [tcr.CloneResidency] Dismiss warnings from pivot_wider

What's Changed

• 🔖 0.14.1 by @pwwang in https://github.com/pwwang/biopipen/pull/58

Full Changelog: https://github.com/pwwang/biopipen/compare/0.14.0...0.14.1

• ⬆️ Bump pipen-board to 0.6.3
• 🔧 Fix make-examples.sh for docker images for pipelines
• 🚑 [scrna_basic] Fix "Issued certificate has expired" in making examples for docker
• ✨ [tcr.CDR3AAphyschem] Add process
• ✨ [cnv.TMADScore] Add TMADScore and TMADScoreSummary
• 🚑 [cnv.TMADScore] Fix wrong envs.seg_transform received in script
• 📝 [cnv.TMADScoreSummary] Add report template
• ✨ [cnv.TMADScoreSummary] Support grouping by 2 groups hierarchically
• 💥 [cnv.AneuploidyScore] Change envs.include_sex to envs.excl_chroms so exclusion of chroms is more flexible
• 🚑 [cnv.AneuploidyScoreSummary] Adjust with of CAA plot based on number of samples
• ✨ [cnv.AneuploidyScoreSummary] Support grouping by 2 groups hierarchically

What's Changed

• 0.14.0 by @pwwang in https://github.com/pwwang/biopipen/pull/57

Full Changelog: https://github.com/pwwang/biopipen/compare/0.13.0...0.14.0

• ⬆️ Bump pipen-board to 0.5.8
• ♻️ [scrna_basic] Change detault tag from dev to master for docker image
• 📝 [scrna_basic] Change detault tag from dev to master in docs
• 🔧 [scrna_basic] Change detault tag from dev to master in entry.sh
• 🔧 [scrna_basic] Fix make-examples.sh when running indenpendently
• 🔧 [scrna_basic] Add plugin_opts.report_no_collapse in board.html
• 🚧 [cnvkit_pipeline] Init docker building
• ⚙️ [cnvkit_pipeline] Make examples
• ⚙️ [cnvkit_pipeline] Update example.json for pipen-board
• 🔧 [cnvkit_pipeline] Fix example in docker image
• 📝 [scrna_metabolic_landscape] Update docstrings to adopt pipen-board
• 📝 [utils.misc] Add docstring for run_command
• 🐛 [cnvkit.CNVkitGuessBaits] Use a better way to determine python of cnvkit.py

What's Changed

• 0.13.0 by @pwwang in https://github.com/pwwang/biopipen/pull/56

Full Changelog: https://github.com/pwwang/biopipen/compare/0.12.0...0.13.0

• ⬆️ Bump pipen to 0.10
• ⬆️ Bump pipen-runinfo to 0.1.1
• ⬆️ Bump pipen-report to 0.12 and pipen-runinfo to 0.2
• ⬆️ Bump pipen-args to 0.10.2
• ⬆️ Bump pipen-board to 0.5.6
• 📝 Use flag instead action=store_true in docstring
• ✅ [utils.gene] Fix tests
• 🎨 [scrna.SeuratMap2Ref] Add envs.MappingScore
• ✨ [scrna.SeuratMap2Ref] Add report template
• 💄 [scrna.SeuratMap2Ref] Make figures in 2 columns in report
• ✨ [scrna.CellTypeAnnotate] Add ScCATCH for cell type annotation
• 🎨 [scrna.CellTypeAnnotate] Warn when no cell types are given
• 🐛 [cnvkit] Fix when some arguments are None
• 📝 [cnvkit_pipeline] Update docstrings to adopt latest pipen-annotate and pipen-board
• 📝 [cnv] Update docstring
• 🚑 [cnv.AneuploidyScoreSummary] Fix when envs.group_col is None but in.metafile is given
• 👷 [scrna_basic] Init docker image building action
• 👷 [scrna_basic] Fix dockhub credentials
• 📝 [scrna_basic] Update docstrings to adopt latest pipen-annotate and pipen-board
• 📝 [scrna_basic] Add documentation
• 🔧 [scrna_basic] Update configuration for docker image building

What's Changed

• 0.12.0 by @pwwang in https://github.com/pwwang/biopipen/pull/55

Full Changelog: https://github.com/pwwang/biopipen/compare/0.11.0...0.12.0

• ⬆️ Bump pipen to 0.9
• ⬆️ Drop support for python3.7
• ➕ Add pipen-board as dependency
• ✨ Add board.toml for pipen-board to run
• 🐛 [cnvkit.CNVkitCoverage] Fix error when generating flat reference
• 🎨 [bed.BedConsensus] Use bedtools genomecov to calculate the consensus regions
• 🐛 [core.filters] Keep list of dict in python as list of list in R
• ✨ [scrna_metabolic_landscape] Allow multiple subsettings for the data
• ✨ [scrna_basic] Initialize the pipeline
• 🐛 [bed.Bed2Vcf] Fix OrderedDiot not found
• 🎨 [cnvkit_pipeline] Import cached_property directly
• 🐛 [scrna.SeuratPerparing] Fix when input contains a single sample
• 🎨 [tests] Use --reuse instead of --former
• 🐛 [vcf.VcfSplitSamples] Fix missing mutations for extract samples
• 🎨 [scrna_metabolic_landscape.MetabolicPathwayHeterogeneity] Add progress indicator
• 🎨 [scrna.SeuratClustering] Allow sample names to be assigned for reference for FindIntegrationAnchors
• 🎨 [scrna_metabolic_landscape.MetabolicPathwayActivity] Add merged heatmaps for subsets
• 🐛 [scrna_metabolic_landscape.MetabolicPathwayIntraSubsets] Fix fetching subsetting_comparison and limit nproc for FGSEA to 1
• 🎨 [scrna_metabolic_landscape.MetabolicPathwayFeatures] Ignore NAs in subsets
• 🎨 [scrna_metabolic_landscape] Adopt pipen-args 0.9.7
• ✨ [scrna.SeuratMap2Ref] Add process
• ➖ [utils] Retire cmdy
• ✨ [bed.BedtoolsMerge] Add process
• 🎨 [core.testing] Use --cache to control of reusing previous run
• 🎨 [csv.BindRows] Allow to add filename
• 📌 [scrna_basic] Adopt pipen-board 0.1.2
• 🐛 [web.Download] Fix when args is Diot
• 🎨 [cnvkit.CNVkitCall] Detach cmdy
• ✨ [bam.BamSplitChroms] Add process
• ✨ [bam.Merge] Add process and test
• 🐛 [core] Fix repr filter in templates for Diot objects
• 🐛 [docs] Add mygene dep for building utils.gene
• ✅ [vcf.TruvariBench] Pin truvari to v3.4.0 for tests

What's Changed

• 0.11.0 by @pwwang in https://github.com/pwwang/biopipen/pull/52

Full Changelog: https://github.com/pwwang/biopipen/compare/0.9.0...0.11.0

• ⬆️ Bump pipen to 0.6

What's Changed

• 0.9.0 by @pwwang in https://github.com/pwwang/biopipen/pull/51

Full Changelog: https://github.com/pwwang/biopipen/compare/0.8.0...0.9.0

• 🚀 [vcf.VcfAnno] Add VcfAnno to use vcfanno to annotate VCF files
• ✨ [tcgamaf.Maf2Vcf] Add Variant_Classification and Variant_Type to output vcf
• ✨ [vcf.VcfFix] Allow gziped vcf as input
• ⬆️ Bump up pipen to 0.5
• 🧹 Remove tests for core pipeline (not needed any more)

What's Changed

• 0.8.0 by @pwwang in https://github.com/pwwang/biopipen/pull/50

Full Changelog: https://github.com/pwwang/biopipen/compare/0.7.1...0.8.0

• ⬆️ Upgrade pipen-filters to 0.2
• 👽️ Adopt pipen-filters 0.2 in reports
• 🔧 Rename scrna_metabolic namespace to scrna_metabolic_landscape in entry points
• ✨ [scrna.MarkersFinder] Add each for cases to run on each value of metadata variable each
• ✨ [tcgamaf.Maf2Vcf] Add proc
• ✨ [bcftools.BcftoolsSort] Add proc

What's Changed

• 0.7.1 by @pwwang in https://github.com/pwwang/biopipen/pull/49

Full Changelog: https://github.com/pwwang/biopipen/compare/0.7.0...0.7.1

• 🧑‍💻 [tcr.Immunarch] Allow separating samples for rarefraction analysis
• ✨ [scrna.SeuratClusterStats] Add expression matrix to output
• 🧑‍💻 [tcr.Immunarch] Allow align_x and log scale for rarefraction analysis
• ✨ [cnv.AneuploidyScoreSummary] Add heatmaps
• 🧑‍💻 [tcr.Immunarch] Allow separating samples for rarefraction analysis
• ✨ [scrna.SeuratClusterStats] Add expression matrix to output
• 🧑‍💻 [tcr.Immunarch] Allow align_x and log scale for rarefraction analysis
• ✨ [cnv.AneuploidyScoreSummary] Add heatmaps
• 🐛 [cnv.Aneuploidy] Fix when only one arm has signals for a chromosome
• ✨ [cnvkit.CNVkitGuessBaits] Add proc
• ♻️ [cnvkit_pipeline] Refactor and add docs
• 🎨 [cnvkit_pipeline] Use process decorator to define processes
• ✨ [scrna.SeuratClusterStats] Allow groupby other metadata column than Sample in cell stats
• ✨ [scrna.ExprImput] Add ALRA and set as default
• 🎨 [scrna.scrna_metabolic_landscape] Move from scrna_metabolic and use Seurat object directly instead of sce
• 🐛 [scrna.SeuratClustering] Fix when there are fewer cells
• ✨ [scrna.CellTypeAnnotate] Add proc and tests
• ✨ [scrna.SeuratClusterStats] Allow subsetting for cell stats
• ✅ [vcf.Vcf2Bed] Fix test
• ✅ [tests] Add refgenes for testing
• 🐛 [tests] Fix reference preparing
• ✅ [tests] Add sctype db for tests
• ✅ [tests] Try not patch using lastest poetry
• ✅ [tests] Build test deps and fix tests
• 👷 [tests] Exclude test_scrna_metabolic_landscape from CI
• ⬆️ Upgrade pipen-cli-run to 0.4.1
• ⬆️ Upgrade pipen to 0.3.11

What's Changed

• 0.7.0 by @pwwang in https://github.com/pwwang/biopipen/pull/48

Full Changelog: https://github.com/pwwang/biopipen/compare/0.6.2...0.7.0