broadinstitute / viral-core
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coverage: 68.291% (+2.5%) from 65.78%
19182396509

Pull #119

github

dpark01 
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 disk and independently reconstructing pool IDs (muxed_run), which could
differ from the pool IDs computed by SampleSheet.inner_demux_mapper(). This
caused FileNotFoundError when searching for splitcode summary JSON files.

Example:
- Expected: AGCGTGTT-CTTCGCAA.l1_summary.json
- Actual:   AGCGTGTT-CTTCGCAA.l1.AAGCG75M5.1_summary.json

Changes:
1. Modified create_splitcode_lookup_table() to accept either a file path
   (legacy behavior) or DataFrame (new behavior)
2. Updated splitcode_demux() to pass inner_demux_barcode_map_df DataFrame
   directly instead of re-reading the sample sheet
3. Added library_id_per_sample to inner_demux_mapper() output columns

This ensures a single source of truth for pool IDs throughout the workflow,
eliminating the pool ID mismatch issue. All 91 unit tests pass.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>
Pull Request #119: Add demultiplexing of 3-barcode sheets with splitcode

1059 of 1372 new or added lines in 8 files covered. (77.19%)

8 existing lines in 1 file now uncovered.

3868 of 5664 relevant lines covered (68.29%)

0.68 hits per line

Relevant lines Covered
5664 RELEVANT LINES 3868 COVERED LINES
0.68 HITS PER LINE
Source Files on ct-swiftseq-demux-integration

Recent builds

Builds Branch Commit Type Ran Committer Via Coverage
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 dpark01 github
68.29
19182397451 ct-swiftseq-demux-integration Merge 4c92054f8 into d3ad25d5f Pull #119 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 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 dpark01 github
62.85
19176241106 ct-swiftseq-demux-integration Consolidate splitcode tests into test_illumina.py - Move all splitcode test classes from test_illumina_splitcode.py to test_illumina.py - Add missing imports (shutil, json, tools.picard) to test_illumina.py - Delete test_illumina_splitcode.py to ... Pull #119 dpark01 github
62.59
19176241878 ct-swiftseq-demux-integration Merge df8d80620 into d3ad25d5f Pull #119 web-flow github
62.61
19175507121 ct-swiftseq-demux-integration Add robust error handling for splitcode summary JSON loading When splitcode summary JSON files are missing or malformed, we now provide comprehensive debugging information to help diagnose the issue faster. Changes to illumina.py (create_splitco... Pull #119 dpark01 github
61.07
19175508368 ct-swiftseq-demux-integration Merge 6465a193a into d3ad25d5f Pull #119 web-flow github
61.07
19175360543 ct-swiftseq-demux-integration Extract splitcode config/keep file generation into testable function - Created generate_splitcode_config_and_keep_files() function to handle config and keep file generation for a single pool - This separates pure text file transformation logic ... push dpark01 github
60.61
19175361248 ct-swiftseq-demux-integration Merge 26cb5b64e into d3ad25d5f Pull #119 web-flow github
60.92
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