biopipen

• 🎨 [scripts.utils.vcf] Use format keys for samples
• ✨ [vcf.VcfFix] Dedent envs.helpers automatically and allow it to be list of strings
• 🧑‍💻 [tcr.CloneResidency] Add count table and allow grouping samples in the report
• 🧑‍💻 [cnvkit.CNVkitCall] Allow not passing threshold
• 🧑‍💻 [cnvkit.CNVkitCall] Allow setting cutoff to fetch significant genes for enrichment analysis
• 🧑‍💻 [scrna.SeuratPreparing/SeuratClustering] Do QC in SeuratPreparing only and prepare clustering in SeuratClustering
• ✨ [cnvkit_pipeline] Allow customization of colnames in metafile
• 💚 Fix CI (conda-incubator/setup-miniconda#274)

What's Changed

• 0.6.2 by @pwwang in https://github.com/pwwang/biopipen/pull/47

Full Changelog: https://github.com/pwwang/biopipen/compare/0.6.1...0.6.2

• ✨ [cnvkit_pipeline] Allow purity for each sample
• ✨ [tcr.ImmunarchSplitIdents] Add proc
• ✨ [vcf.VcfSplitSamples] Add proc
• 🏗️ [cnvkit.CNVkitCall] Pass purity as input instead of envs
• ✨ [vcf.VcfIntersect] Add proc
• ✨ [vcf.VcfSampleSplits] Add envs.private to keep only private sites for each sample
• 🔧 Fix setup.py file type
• ✅ Fix tests for utils.gene
• 🚨 Ignore template strings in python scripts for pyright

What's Changed

• 🔖 0.6.1 by @pwwang in https://github.com/pwwang/biopipen/pull/46

Full Changelog: https://github.com/pwwang/biopipen/compare/0.6.0...0.6.1

• ✨ [cnv] Add AneuploidyScore and AneuploidyScoreSummary
• ✨ [scrna.Write10X] Add Write10X
• ✨ [cnv.AneuploidyScore] Add envs.include_sex
• 🐛 [scrna.SeuratSubset] Fix when envs.groupby is not given
• ✨ [cnvkit.CNVkitHeatmap] Add envs.order for sample order in the heatmap
• ✨ [bam.CNAClinic] Add bam.CNAClinic
• ✨ [bam.CNAClinic] Add report
• ✨ [cnv.AneuploidyScore] Allow a list of thresholds for envs.cn_transform
• ✨ [scrna.SeuratSplit] Add scrna.SeuratSplit
• ✏️ [core] Fix typo in core.proc.Pipeline
• 👽️ Refactor pipeline modules with pipen-cli-run 0.3
• 💚 Use mamba in CI

• ✨ [scrna.SeuratClusterStats] Allow features to be a file for expression plots
• ✨ [tcr.CloneSizeQQPlot] Add process
• 🩹 [tcr.Immunarch] Fix bad characters in the “Motif Analysis” section in report (#43)

What's Changed

• 0.5.3 by @pwwang in https://github.com/pwwang/biopipen/pull/44

Full Changelog: https://github.com/pwwang/biopipen/compare/0.5.2...0.5.3

• ⬆️ Pump pipen-args to 0.3
• 🩹 [scrna.CellsDistribution] Filter NA cells.by

0.5.1

• 💚 Fix CI
• 🚨 Add and fix linting
• ⬆️ Pump pipen-report to 0.4.5

0.5.0 (skipped due to CI failure)

• ✅ [vcf.VcfFix] Add chrom size fixes
• ✨ [utils.reference] Add bam_index
• 🐛 [bam.CNVpytor] Fix vcf-fix only adds last contig and fix header with snp data
• ✨ [vcf.Vcf2Bed] Add process and test
• 🐛 [bed.BedConsensus] Fix final weighting issue
• 🩹 [All] Use %>% instead of |> in all R scripts for backward compatibility
• 🐛 [scrna_metabolic] Don't turn "Ident" to "seurat_clusters" for grouping.groupby in config
• 🏗️ [tests] Add prefix "biopipen-" to conda environment names
• ✅ [tests] Enable pipen-report only when necessary

What's Changed

• 0.5.0 by @pwwang in https://github.com/pwwang/biopipen/pull/40
• 0.5.1 by @pwwang in https://github.com/pwwang/biopipen/pull/41

Full Changelog: https://github.com/pwwang/biopipen/compare/0.4.9...0.5.1

• 👷 [test] Reverse immunarch in env_r
• ✨ [bam.CNVpytor] Add filters
• ✨ [cnvkit/cnvkit_pipeline] Add processes and pipeline
• 🐛 [bam.cnvkit] Fix filter direction
• 🚑 [scrna_metabolic] Fix nproc for runFGSEA for MetabolicPathwayHeterogeneity

What's Changed

• 0.4.9 by @pwwang in https://github.com/pwwang/biopipen/pull/39

Full Changelog: https://github.com/pwwang/biopipen/compare/0.4.8...0.4.9

• 🩹 [core] Add default for config.exe.bedtools
• 🩹 [scrna.ScFGSEA] Don't convert sparse matrix to avoid "problem too large" error

What's Changed

• 0.4.8 by @pwwang in https://github.com/pwwang/biopipen/pull/38

Full Changelog: https://github.com/pwwang/biopipen/compare/0.4.7...0.4.8

• 🐛 [scrna.SeuratPreparing] Fix new data preparing when errored

What's Changed

• 0.4.7 by @pwwang in https://github.com/pwwang/biopipen/pull/37

Full Changelog: https://github.com/pwwang/biopipen/compare/0.4.6...0.4.7

• ✨ [vcf.TruvariBench] Allow multimatch to be passed
• ✨ [vcf.TruvariConsistency] Add report

• ✨ [bam.CNVpytor] Generate and fix VCF file as result
• 📝 [vcf.TruvariBench] Update docs to show other arguments for truvari bench
• ✨ [vcf.TruvariBench] Allow sizemax to be passed
• ✨ [bed.BedConsensus] Add process and tests
• ✨ [core] Add ref.genome to configurations
• ⚡️ [bed.BedConsensus] Parallelize and speed up
• 💚 [test] Add bedtools to env bio
• 💚 [test] Add chromsome sizes to reference
• 💚 [test] Add r-gsea_r to env r
• 💚 [scrna.ScFGSEA] Fix tests

What's Changed

• 0.4.5 by @pwwang in https://github.com/pwwang/biopipen/pull/35

Full Changelog: https://github.com/pwwang/biopipen/compare/0.4.4...0.4.5

• 🐛 [scrna.SeuratPreparing] Fix after tidyseurat being used
• 🐛 [scrna.SeuratPreparing] Fix object Sample not found
• 📝 [Housekeeping] Fix API docs
• 📝 [Housekeeping] Make apis show neater docs

What's Changed

• 0.4.4 by @pwwang in https://github.com/pwwang/biopipen/pull/34

Full Changelog: https://github.com/pwwang/biopipen/compare/0.4.3...0.4.4

• ✨ [scrna] Add filter for cases in CellsDistribution, MarkersFinder and ScFGSEA
• ✨ [utils] Allow gg object for ggs in plot.R
• 🐛 [scrna_metabolic] Fix reports
• 🐛 [scrna_metabolic] Fix multiple cases
• 🐛 [scrna_metabolic] Fix rmagic for normalization
• ⚡️ [scrna.SeuratClusterStats] Add common gene list
• ⚡️ [scrna.MarkersFinder] Add filter2 to filter after mutaters
• 🐛 [tcr.Immunarch] Fix missing library tibble in script
• ⚡️ [scrna.ScFGSEA] Make ident hierarchical

What's Changed

• 0.4.3 by @pwwang in https://github.com/pwwang/biopipen/pull/33

Full Changelog: https://github.com/pwwang/biopipen/compare/0.4.2...0.4.3

• 💚 [Housekeeping] Fix CI deploy
• ⚡️ [processes] Use faster do_call() instead of do.call()
• 📝 [tcr] Fix some docstrings with {{ and }}
• ✅ [vcf.TruvariBench] Add ref for test
• 🩹 [tcr.TCRClustering] FIx VGeneScores.txt being generated in current dir
• 📝 [scrna.SeuratPreparing] Update docstring and refactor script
• ✨ [scrna.SeuratClustering] Allow dims to be expanded in arguments
• 📝 [scrna.MarkersFinder] Adopt reduced case configuration level

What's Changed

• 0.4.2 by @pwwang in https://github.com/pwwang/biopipen/pull/32

Full Changelog: https://github.com/pwwang/biopipen/compare/0.4.1...0.4.2

0.4.1

General

• 👷 [Housekeeping] Add deploy in CI
• 🚚 [Housekeeping] Move tests/test_tcr/TCRClustering to tests/test_tcr/TCRClusteringStats
• 🔧 [Tests] Add r-tidyseurat to env_r.toml

Processes

• 🩹 [scrna.CellsDistribution] Reduce envs.cases levels
• 🩹 [scrna.CellsDistribution] Allow acurate sizes to be used in orderby
• 🩹 [scrna.ScFGSEA] Reduce envs.cases levels
• ✨ [scrna.ScFGSEA] Allow {ident} or {cluster} as placeholder in cases
• ✨ [scrna.SeuratClusterStats] Add dimplots
• 🚑 [scrna.SeuratClusterStats] Limit 20 genes by default
• 🐛 [tcr.ImmunarchLoading] Fix multiple "Source" columns in data
• 🩹 [tcr.TCRClustering] Make clusterfile as a meta file that can be used by SeuratMetadataMutater
• ✨ [tcr.TCRClusteringStats] Add shared clusters by grouping
• 📝 [tcr.TCRClusteringStats] Don't show shared TCR clusters between groups if not configured
• 📝 [gsea.FGSEA] Limit pagesize to 10 in report
• ✨ [vcf.TruvariBenchSummary] Add process and test
• ✨ [vcf.TruvariBenchSummary] Add default input_data
• ✏️ [bed.Bed2Vcf] Fix typos in doc
• ✨ [bed.Bed2Vcf] Allow records to be skipped
• ✅ [vcf.TruvariBench] Add ref for test

What's Changed

• 0.4.1 by @pwwang in https://github.com/pwwang/biopipen/pull/31

Full Changelog: https://github.com/pwwang/biopipen/compare/0.4.0...0.4.1

• ✨ [scrna.CellsDistribution] Add process and test
• 🗑️ Remove namespaces (use ns instead)

• ✅ Allow tests to run locally only
• 💚 Add pipen-args for tests
• ✅ [plot.Heatmap] Fix test
• ✅ [pipeline.scrna_metabolic] Add ARGS in run.env
• ✅ [scrna.ScFGSEA] Add test
• ✨ [tcr.TCRClusteringStats] Add process
• ✅ [tcr.TCRClustering] Use env r for testing
• ✅ [tcr.TCRClustering] Add test
• ✅ [pipeline.scrna_metabolic] Add test
• ✅ [gsea.GSEA] Add tests
• ✅ [gsea.FGSEA] Add tests
• ✅ [plot.Heatmap] Add tests
• ✅ [gene.GeneNameConversion] Add tests
• ✅ [utils.gene] Add tests
• 💚 [bed.Bed2Vcf] Fix test
• ✅ [vcf.VcfFix] Add test
• ✅ [misc.File2Proc] Use base container for test
• ✅ [misc.File2Proc] Fix test
• 🩹 [scrna.ExprImpute] Use if-statement for requirements
• ✨ [scrna.SeuratClusterStats] Add process and test

• 🗑️ Deprecate biopipen.namespaces, use biopipen.ns instead
• ✨ [bed.Bed2Vcf] Add bed.Bed2Vcf
• ✨ [vcf.VcfFix] Add vcf.VcfFix
• 🐛 [vcf.vcfFix] Fix when a flag in INFO
• ✨ [vcf.TruvariBench] Add vcf.TruvariBench
• ✨ [vcf.TruvariConsistency] Add vcf.TruvariConsistency
• 🐛 [utils.reference] Fix typo in tabix_index
• 🐛 [vcf.VcfIndex] Fix vcf.VcfIndex
• ✨ [bed.Bed2Vcf] Allow to ignore non-existing contigs and index the output file
• ✨ [misc.Shell] Add misc.Shell to run a shell command

• ♻️ Refactor some processes for immunopipe
• 🩹 [scrna.SeuratPreparing] Remove tmp datadir for scrna.SeuratPreparing if exsits
• 🩹 [scrna.SeuratPreparing] Add a TODO comment in scrna.SeuratPreparing (#26)
• ✨ [scrna.Subset10X] Add scrna.Subset10X
• 💥 [tcr.Immunarch] Merge tcr.ImmunarchBasic and tcr.ImmunarchAdvanced into tcr.Immunarch
• 🩹 [tcr.VJUsage] Fix R script being generated at current direct for tcr.VJUsage
• ✨ [scrna.SeuratMetadataMutater] Add scrna.SeuratMetadataMutater
• 🐛 [tcr.Immunarch] Fix clonotype tracking not selecting top clones by given top N
• ♻️ [pipeline.scrna_metabolic] Refactor scrna_metabolic
• 📝 [pipeline.scrna_metabolic] Update docs for scrna_metabolic pipeline
• ✨ [pipeline.scrna_metabolic] Allow scrna_metabolic pipeline to handle multiple cases
• 🚑 [scrna.ExprImpute] Fix reticulate not using right python
• 🚑 [scrna.SeuratMetadataMutater] Fix error when input mutaters in None
• 🚑 [scrna_metabolic.MetabolicInputs] Fix diot not imported in script
• ✅ [0.3.0] Add test outline

What's Changed

• 0.2.1 by @pwwang in https://github.com/pwwang/biopipen/pull/24

  • User rtoml over toml

Full Changelog: https://github.com/pwwang/biopipen/compare/0.2.0...0.2.1