v2.0.0

2.0.0 (2025-11-05)

⚠ BREAKING CHANGES

• now really bump major version

Features

• double-check that multiplexing TSV specifies barcodes for all samples in a pool and otherwise provide useful error message (fc334ad)

Bug Fixes

• adjust expected files to example run (removed some files that are listed in cellranger multi documentation, and added three that I didn't see anywhere there, but that got generated) (e04008d)
• adjust files and tests to allow for multiplexing setup and configuration (fa65baa)
• adjust multi config csv creation to account for multiplexing (a0b1ca6)
• allow for non-existent output directory before first cellranger multi run (2f26c90)
• also cover Antigen Capture output in multiplexing (71f9d02)
• also remove cloupe file from final output (7e8616f)
• also use the correctly named bash script with .sh suffix (f19244e)
• anyOf required syntax for multiplexing_sheet.schema.yaml (44265a7)
• bugs in bash script for file existence check and touch, apply suggestions by coderabbitai (dd35c50)
• catch case where pool id is not present in multiplexing TSV file (ce1426d)
• check for file existence before touching files in cellranger output check rules (28adf06)
• cloupe just doesn't get created (maybe it's part of secondary analyses?) (714972d)
• coderabbitai nitpicks (97b3a22)
• debug overhauled multi condig CSV script (a54ff65)
• default lookups to None, instead of using dummy input files (11dc7ff)
• disable telemetry during cellranger installation (2bed667)
• example pools.tsv still had sample column (1177848)
• explicitly load used packages, to fail early if not available (edadfe4)
• first batch of dryrun fixes (f090230)
• handle case of a single sample for a pool ID (fd6db2e)
• improve pool_sheet schema wording (066ceeb)
• include and validate multiplexing_sheet schema (aee4e1a)
• include multiplexing sheet handling (bb121cc)
• indentation of config.schema.yaml (7626f88)
• initial dryrun fixes done (ce35b5a)
• initial file setup for Gene Expression and VDJ data, not yet handled in final rule input request (04adb4f)
• initial setup to determine final output dynamically (5751e4a)
• load and validate multiplexing sheet outside of input function (globally) (ae4a29a)
• make all cellranger output check rules explicitly update() output files, to avoid deletion (0581fee)
• make pool_samples extraction work (cee3ffc)
• more testing fixes (ae79478)
• move schemas into workflow directory (8cb7b63)
• name arguments in branch() function (1b77dd4)
• now really bump major version (d85d1d2)
• proper snakemake object usage in R (3331e2a)
• provide conda environment for every rule (use coreutils, which provides the used touch command) (2e143e2)
• R syntax (c519b68)
• rename bash script to expected .sh suffix (18cd495)
• rename example samples.tsv to pools.tsv (9a2d996)
• switch back to proper CSV placeholder for feature: reference: path (0c6e6d3)
• switch to specifying samples in multiplexing TSV file, rename samples.tsv files to pools.tsv (67c1f9c)
• switch to using pool_sheet instead of sample_sheet everywhere in the code (1b439e8)
• try tracking main out_dir instead of cellranger's outs/ subdirectory in cellranger_multi_run (ef91bcc)
• typo (2625eab)
• typo in multiplexing.tsv header (f4bca14)
• update config.schema.yaml (55371d8)
• use empty list instead of None for optional input (d1a8719)
• wildcard constraint for vdj_type (c82a68b)

Performance Improvements

• increase default threads for cellranger multi to 16 (0367ac6)
• make no-secondary: "true" the default in config/config.yaml (94be12d)
• make everything except cellranger multi a localrule (fda1a9e)

v1.0.1

1.0.1 (2025-10-28)

Bug Fixes

• absolute sample folder paths (41c7ac6)
• comment out cell-annotation-model: auto in example config/config.yaml, to avoid an unintended 10X cloud authentication requirement (62f375b)
• fastqs folder parsing and vdj reference path docs (ebba69a)
• fastqs folder parsing from input files (b678734)
• filename for cellranger without assay type (98ff5e3)

v1.0.0

1.0.0 (2025-10-22)

Features

• add cellrange count web summary to report (02efb6b)
• add cellranger install from CELLRANGER_TARBALL envvar (46afa34)
• initial ci testing setup (93229e4)
• initial config setup and first wave of changes for cellranger multi (261a240)
• initial script version for multi config csv creation (should contain all the necessary logic, not yet tested) (39fcbf6)
• initial workflow version, untested (6693269)
• working dryrun GitHub Actions test (6e666a0)

Bug Fixes

• .test/config/samples.tsv read2 to R2 (copy-pasta leftover) (04f3e13)
• actually write output to log file (7e431db)
• add another missing comma (d84a03f)
• add empty resources/refdata directory with .gitignore, so that the dryrun doesn't have a missing input exception (c7e8baa)
• add missing comma (5158e69)
• adjust multi config csv creation to automatically read feature reference file for mhc_alleles (64df05f)
• antigen-specificity parsing (04429d1)
• assign lane_numbers sample_sheet loc lookup (ec31e3c)
• better line spacing (bf3615f)
• bring back accidentally deleted control_ids level under antigen-specificity: in config.yaml (35bbd05)
• cellranger_count output file names (c95a490)
• column heading in third ci test sample sheet (fa33b0e)
• conda env name (94063e4)
• correct authors for the workflow after fork (0c817be)
• correct outs-path adjustment (0a5883f)
• correctly add NA column with bind_rows, only if column does not exist (9c888cd)
• correctly handle snakemake's list structure during R enframe (760270f)
• correctly invoke input function get_input_files (04703f8)
• correctly reference column in sample_sheet (1f3b9cc)
• correctly reference wildcard (b4862c8)
• create meaningful rule all (307bb30)
• delete snakemake-created output dir, to allow cellranger to create it anew (and stop it from complaining about it not being a pipestance, sigh) (7dcfa05)
• dummy placeholder for feature_reference in multi config csv rule (f0b8022)
• ensure lane_number exists for libraries table parsing (ffdf36f)
• ensure that conda bin/ directory is created, even for the empty environment (d627946)
• fastqs path parsing now returns full input path (090b3fe)
• feature_types matching logic in R script (ac80c13)
• fine-tune .gitignore (6cba839)
• import math (f504424)
• initial cellranger_multi rule adaptation (33c69d3)
• lane_number default (bc098a5)
• lane_number lookup (623efd3)
• lane_number lookups and require relative input paths (better portability) (1db14f9)
• load correct smk file (f4b97b2)
• make params.mem_gb for --localmem cl argument an int instead of a float (662ca77)
• more comprehensive samples.tsv (69970c8)
• move sample filtering to after library_type column creation (8dabf74)
• NA_character_ was missing trailing underscore (b51eef6)
• omit secondary cellranger analyses (clustering et al.) (0aed413)
• parse all sample_sheet columns as str (2bca1ef)
• path string generation in get_all_samples_fastq (8bf77c5)
• properly determine lane number in cellranger_count intput (5df7ca9)
• quick and dirty fix to get rid of NA row (74c10a1)
• reference to samples, change to sample_sheet (8aadb28)
• remaining un-replaced library_csv occurrences to multi_config_csv (891cf0e)
• removal of empty mhc_allele columns (cbf7823)
• remove .cloupe file that does not get generated with --nosecondary flag (aa9bded)
• remove empty entries (c5d9fbb)
• remove leftover from template (519735d)
• remove leftover from template workflow (b187dae)
• remove lookups within input functions, if ithey're not in the return statement (765dae3)
• remove multiext because it would be unsupported multi-level (ac5e5f2)
• remove whitespace from wildcards and f...