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feat(eqtl): add eQTL demo script and run pipeline
- Created scripts/eqtl/run_eqtl_demo.py with synthetic data generation - Ran cis-eQTL scan: 3,680 tests, 96 eGenes, 3,584 significant eQTLs - Generated volcano, summary, and boxplot visualizations - Output in output/eqtl/amellifera/{results,plots,logs}/
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‎output/amalgkit/apis_mellifera_all/work/quant/DRR333187/run_info.json‎

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"start_time": "Thu Feb 5 09:28:41 2026",
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"call": "kallisto quant -i output/amalgkit/apis_mellifera_all/work/index/Apis_mellifera_transcripts.idx -o output/amalgkit/apis_mellifera_all/work/quant/DRR333187 -t 2 /Volumes/blue/data/apis_mellifera/DRR333187/DRR333187_1.fastq.gz /Volumes/blue/data/apis_mellifera/DRR333187/DRR333187_2.fastq.gz"
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‎output/amalgkit/apis_mellifera_all/work/quant/SRR072891/run_info.json‎

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"start_time": "Thu Feb 5 09:31:20 2026",
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"call": "kallisto quant -i output/amalgkit/apis_mellifera_all/work/index/Apis_mellifera_transcripts.idx -o output/amalgkit/apis_mellifera_all/work/quant/SRR072891 -t 2 --single -l 200 -s 30 /Volumes/blue/data/apis_mellifera/SRR072891/SRR072891.fastq.gz"
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‎output/amalgkit/apis_mellifera_all/work/quant/SRR14494789/run_info.json‎

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"call": "kallisto quant -i output/amalgkit/apis_mellifera_all/work/index/Apis_mellifera_transcripts.idx -o output/amalgkit/apis_mellifera_all/work/quant/SRR14494789 -t 2 /Volumes/blue/data/apis_mellifera/SRR14494789/SRR14494789_1.fastq.gz /Volumes/blue/data/apis_mellifera/SRR14494789/SRR14494789_2.fastq.gz"
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‎output/amalgkit/apis_mellifera_all/work/quant/SRR14494791/run_info.json‎

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"call": "kallisto quant -i output/amalgkit/apis_mellifera_all/work/index/Apis_mellifera_transcripts.idx -o output/amalgkit/apis_mellifera_all/work/quant/SRR14494791 -t 2 /Volumes/blue/data/apis_mellifera/SRR14494791/SRR14494791_1.fastq.gz /Volumes/blue/data/apis_mellifera/SRR14494791/SRR14494791_2.fastq.gz"
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}

‎output/amalgkit/apis_mellifera_all/work/quant/SRR15204500/run_info.json‎

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"call": "kallisto quant -i output/amalgkit/apis_mellifera_all/work/index/Apis_mellifera_transcripts.idx -o output/amalgkit/apis_mellifera_all/work/quant/SRR15204500 -t 2 --single -l 200 -s 30 /Volumes/blue/data/apis_mellifera/SRR15204500/SRR15204500.fastq.gz"
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‎output/amalgkit/apis_mellifera_all/work/quant/SRR17408939/run_info.json‎

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"call": "kallisto quant -i output/amalgkit/apis_mellifera_all/work/index/Apis_mellifera_transcripts.idx -o output/amalgkit/apis_mellifera_all/work/quant/SRR17408939 -t 2 --single -l 200 -s 30 /Volumes/blue/data/apis_mellifera/SRR17408939/SRR17408939.fastq.gz"
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‎output/amalgkit/apis_mellifera_all/work/quant/SRR26149870/run_info.json‎

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"call": "kallisto quant -i output/amalgkit/apis_mellifera_all/work/index/Apis_mellifera_transcripts.idx -o output/amalgkit/apis_mellifera_all/work/quant/SRR26149870 -t 2 --single -l 200 -s 30 /Volumes/blue/data/apis_mellifera/SRR26149870/SRR26149870.fastq.gz"
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}

‎output/amalgkit/apis_mellifera_all/work/quant/SRR6727845/run_info.json‎

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"call": "kallisto quant -i output/amalgkit/apis_mellifera_all/work/index/Apis_mellifera_transcripts.idx -o output/amalgkit/apis_mellifera_all/work/quant/SRR6727845 -t 2 /Volumes/blue/data/apis_mellifera/SRR6727845/SRR6727845_1.fastq.gz /Volumes/blue/data/apis_mellifera/SRR6727845/SRR6727845_2.fastq.gz"
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‎output/amalgkit/apis_mellifera_all/work/quant/SRR8121093/run_info.json‎

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"call": "kallisto quant -i output/amalgkit/apis_mellifera_all/work/index/Apis_mellifera_transcripts.idx -o output/amalgkit/apis_mellifera_all/work/quant/SRR8121093 -t 2 --single -l 200 -s 30 /Volumes/blue/data/apis_mellifera/SRR8121093/SRR8121093.fastq.gz"
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}

‎output/amalgkit/apis_mellifera_all/work/quant/SRR8121117/run_info.json‎

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"start_time": "Thu Feb 5 09:27:17 2026",
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"call": "kallisto quant -i output/amalgkit/apis_mellifera_all/work/index/Apis_mellifera_transcripts.idx -o output/amalgkit/apis_mellifera_all/work/quant/SRR8121117 -t 2 --single -l 200 -s 30 /Volumes/blue/data/apis_mellifera/SRR8121117/SRR8121117.fastq.gz"
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}

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