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Commits on Feb 11, 2025

• Parallelize split_fastq and compress_fastq over read orientation

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Commits on Feb 10, 2025

• Support multiple FASTQ files per sample and orientation in samples.json

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Commits on Feb 8, 2025

• Update dag.pdf, filegraph.pdf, rulegraph.pdf

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• Bug fix: allow custom output directory (addresses issue #3)

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• fix typo from previous commit

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• Support validation for barcode config file (config.txt) and samples file

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• Bug fix: make sure splitbam_statistics.txt is generated by pipeline

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• Update dag.pdf, filegraph.pdf, and rulegraph.pdf

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• Add Nature Genetics publication reference!

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• Properly escape backslashes in Snakefile.

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• Bug fix: correct sorting for bedtools intersect when applying blacklist mask

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Commits on Feb 7, 2025

• Fix bug where original read name could affect demultiplexing

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• Parallelize bigWig generation over antibody targets.

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• Support different bigWig normalization strategies and improve effective

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Commits on Feb 6, 2025

• rename_and_filter_chr.py now supports renaming and filtering FASTA files

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• Simplify AutoCloseGzipFile implementation

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• Fix file_open() bug that left a file descriptor unclosed

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Commits on Jan 28, 2025

• Update chipdip.yaml environment

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• Add cluster statistics file MD5 hash to pipeline verification script.

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Commits on Jan 25, 2025

• Minor fixes based on Pylance

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Commits on Dec 11, 2024

• Add MacBook Air 15 (Apple M2) to benchmark.

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• Add Mac support

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Commits on Oct 18, 2024

• Update README.md

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Commits on Aug 13, 2024

• Update pipeline benchmarks with Intel i5-4300U data

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Commits on Aug 12, 2024

• Add openjdk to chipdip.yaml. Update Snakefile and README.

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Commits on Aug 9, 2024

• Add more software dependency details to README

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Commits on Aug 7, 2024

• Clarify Bash version requirements in README

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• Update README with pipeline benchmarks from GitHub Codespaces

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• Add export PYTHONNOUSERSITE=True to run_pipeline.sh

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• Update README with system requirements and benchmarks.

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• Update envs/chipdip.yaml to include matplotlib and fix dependency issue.

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Commits on Aug 6, 2024

• Update example data validation script. Remove unnecessary test files.

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Commits on Jul 26, 2024

• Add additional resources (including link to barcoding uniqueness calculator) to README

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• Fix bug in rename_and_filter_chr.py: handle case if reference sequence name of paired read is not in chrom_map

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Commits on May 23, 2024

• Add tests to compare pipeline output to reference output

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