71 lines
1.5 KiB
Bash
71 lines
1.5 KiB
Bash
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#!/bin/bash
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# Test RNA-seq Alignment
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set -e
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echo "=== RNA-seq Align Test ==="
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# Activate environment
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source ~/miniconda3/etc/profile.d/conda.sh
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conda activate rnaseq
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cd /home/xia-lab/wutx/00test/bbav20311
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# Setup test directories
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TEST_JOB="test_align_$(date +%s)"
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WORKSPACE="workspace/${TEST_JOB}"
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INPUT_DIR="${WORKSPACE}/input"
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FINAL_DIR="${WORKSPACE}/final"
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ALIGN_DIR="${WORKSPACE}/rnaseq_align"
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mkdir -p "${INPUT_DIR}" "${FINAL_DIR}" "${ALIGN_DIR}"
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# Copy clean reads from previous QC test
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cp workspace/job_1773836437033/final/SRR6847697_1.clean.fastq.gz "${FINAL_DIR}/"
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cp workspace/job_1773836437033/final/SRR6847697_2.clean.fastq.gz "${FINAL_DIR}/"
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# Create sample config
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cat > "${INPUT_DIR}/samples.yaml" << EOF
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samples:
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SRR6847697:
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- SRR6847697_1.clean.fastq.gz
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- SRR6847697_2.clean.fastq.gz
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EOF
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# HISAT2 index
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HISAT2_INDEX="/home/xia-lab/wutx/00test/bbav2.0302/workspace/rnaseq_test/Ft.genome"
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echo "Input files:"
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ls -lh "${FINAL_DIR}/"
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echo ""
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echo "Running RNA-seq Align..."
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python apps/cli/run_rnaseq_align.py \
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-i "${FINAL_DIR}" \
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-x "${HISAT2_INDEX}" \
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-o "${ALIGN_DIR}" \
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-j "${TEST_JOB}" \
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-p "Ft.SPL" \
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-t 4 \
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--sample-config "${INPUT_DIR}/samples.yaml"
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echo ""
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echo "=== Results ==="
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echo "Final directory:"
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ls -lh "${FINAL_DIR}/"
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echo ""
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echo "Align directory:"
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ls -lh "${ALIGN_DIR}/"
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echo ""
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echo "Manifest:"
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cat "${FINAL_DIR}/Ft.SPL.rnaseq_align.manifest.json" | head -50
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echo ""
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echo "Report:"
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cat "${FINAL_DIR}/Ft.SPL.rnaseq_align_report.md"
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echo ""
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echo "=== Test Complete ==="
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