19233671879

Builds	Branch	Commit	Type	Ran	Committer	Via	Coverage
19233671879	ct-swiftseq-demux-integration	Normalize barcodes before comparison (GitHub Copilot comment #2510390253) Apply normalize_barcode() to both FASTQ header barcodes and samplesheet barcodes before comparison. This defensive fix ensures the code handles: - Lowercase barcodes in sam...	Pull #123	10 Nov 2025 01:54PM UTC	dpark01	github	69.32
19233175818	ct-swiftseq-demux-integration	Fix demux_metrics.json schema inconsistency (GitHub Copilot comment #2510390266) Make the 2-barcode and 3-barcode branches use a consistent schema format for demux_metrics.json. Both now use the nested structure: { "demux_type": "...", "samp...	Pull #123	10 Nov 2025 01:36PM UTC	dpark01	github	69.49
19232913568	ct-swiftseq-demux-integration	Fix two code review issues from GitHub Copilot (PR #123) 1. Fix collapsibility check to use filtered samples only (comment #2510390315) - Bug: was checking can_be_collapsed on entire samplesheet - This incorrectly rejected valid 3-barcode p...	push	10 Nov 2025 01:27PM UTC	dpark01	github	69.49
19232528747	ct-swiftseq-demux-integration	Update illumina.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>	Pull #123	10 Nov 2025 01:13PM UTC	web-flow	github	69.45
19232523278	ct-swiftseq-demux-integration	Update illumina.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>	push	10 Nov 2025 01:13PM UTC	web-flow	github	69.28
19231826473	ct-swiftseq-demux-integration	Document SwiftSeq demultiplexing support in DEVELOPMENT_NOTES.md Add section describing the new illumina_metadata and splitcode_demux_fastqs commands for handling DRAGEN FASTQ format with barcodes in headers. This provides developers with contex...	Pull #123	10 Nov 2025 12:47PM UTC	dpark01	github	69.21
19220027161	ct-swiftseq-demux-integration	Add RunInfo.xml support to splitcode_demux_fastqs for richer BAM metadata - Add optional runinfo parameter (default None) - Change sequencing_center default from 'Broad' to None - Populate BAM headers with richer metadata: - RUN_DATE from runIn...	Pull #123	10 Nov 2025 04:03AM UTC	dpark01	github	69.28
19220027547	ct-swiftseq-demux-integration	Merge 832ed24f0 into c6f838b46	Pull #123	10 Nov 2025 04:01AM UTC	web-flow	github	69.45
19203237143	master	Merge pull request #124 from broadinstitute/dp-fix-fastqc Fix fastqc to produce valid empty zip file for empty BAM inputs	push	09 Nov 2025 04:29AM UTC	web-flow	github	68.57
19203125928	dp-fix-fastqc	Merge 80dac80fe into 87dfa212e	Pull #124	09 Nov 2025 04:17AM UTC	web-flow	github	68.58
19193698996	master	Merge pull request #119 from broadinstitute/ct-swiftseq-demux-integration Add demultiplexing of 3-barcode sheets with splitcode	push	08 Nov 2025 01:40PM UTC	web-flow	github	68.27
19182396509	ct-swiftseq-demux-integration	Fix pool ID mismatch bug in splitcode demux Fixes Terra workflow failures where splitcode summary JSON files could not be found due to mismatched pool identifiers. Root cause: create_splitcode_lookup_table() was re-reading the sample sheet from ...	Pull #119	07 Nov 2025 10:13PM UTC	dpark01	github	68.29
19182397451	ct-swiftseq-demux-integration	Merge 4c92054f8 into d3ad25d5f	Pull #119	07 Nov 2025 10:12PM UTC	web-flow	github	68.0
19181447632	ct-swiftseq-demux-integration	Fix splitcode 0.31.4 compatibility: use Unix line endings in config/keep files Splitcode 0.31.4 no longer strips carriage returns from IDs in config/keep files, causing output files to be created with \r in filenames (e.g., Sample1\r_R1.fastq ins...	Pull #119	07 Nov 2025 09:27PM UTC	dpark01	github	68.03
19177273718	ct-swiftseq-demux-integration	Fix three-barcode demux bug: Use full pool ID for splitcode JSON lookup Fixes FileNotFoundError when looking up splitcode summary JSON files in workflows with append_run_id (e.g., flowcell IDs). Root cause: Code was stripping run suffix from poo...	Pull #119	07 Nov 2025 06:26PM UTC	dpark01	github	62.85

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